The first thing is to put the crankshaft (the bottom pulley) and the camshaft (the top pulley) in ABOUT the right position. What you are striving for is to get the engine so it is at TDC (Top Dead Center) on the #1 (front of the engine) piston.
1. Crankshaft #1 cylinder TDC: Pull the spark plug closest to the front of the engine. (Turning the engine manually will be easier if you also back off the other spark plugs, but it isn't absolutely necessary...and if you DO want to remove all 4 be sure to mark the wires so you know which to put back where afterwards.) Put a socket on the nut of the crankshaft pulley, and rotate it clockwise as viewed from the front of the engine, while shining a strong flashlight into the spark plug hole. You should be able to see the top of the piston as it moves up in the cylinder. The goal is to position the piston so it is at the absolute highest point. The piston will rise quickly then slow down as it reaches the top, and then will slowly start to descend again. Move your crankcase wrench back and forth so the piston is in the middle of what seems to be the highest point. ALTERNATE to flashlight if you can't see it: Put a thin bladed screwdriver in the spark plug hole while you GENTLY move the crankcase. The piston will push the screwdriver up as it rises in the bore so again you can find the highest point. BE CAREFUL, you don't want to gouge the top of the piston or wedge the screwdriver...but this really isn't difficult...and I would generally use the screwdriver method myself. OK one way or another the piston should now at the top of its travel, and the crankcase pulley will be within a few degrees of where you want...more to follow on this later.
2. Camshaft #1 cylinder positioning: When the crankshaft is at TDC on it's firing cycle, the two valves on the #1 cylinder will both be closed, and the distributer rotor will be pointing (about) to the #1 spark plug wire. To check all this, remove the valve cover (4 bolts) if you haven't already done so. The hose from the air filter will just pull off. Loosen the 4 bolts that stick up through the sheetmetal valve cover, and pull off the cover. It may stick a bit..tap gently with a mallet to loosen it. You may have a little trouble working the cover past the protrusions and off the engine, but wiggle it around a bit and you can do so. (Note for reassembly: Make sure the gasket is in place and not wrinkled or torn when reassembling.) Take a look at your distributor...one of the posts has the wire on it that goes to the front (#1 cylinder) sparkplug. There may be a #1 embossed in the cap, maybe not. In any case loosen the two spring clips that hold the distributor cap in place and pull the cap off. You will see the rotor, and one end of it has a brass or copper piece that you want to be pointing right to where the #1 spark plug wire gets attached. To get to this point, rotate the camshaft (top pulley) clockwise (as viewed from the front of the engine) while watching the rotor go around. Also watch the two front valves (one on the driver side, (the exhaust), and one on the passenger side (the intake). You want NEITHER of them to be pressed down by the camshaft lobes. Go ahead and rotate the camshaft a few times while watching the motions of the rocker arms over the valves and the distributor rotor. You will get a sense of how things go up and down and around...and when BOTH valve rockers are in the up position for the front cylinder, and the rotor is pointing to the #1 spark plug wire connector, you are within a few degrees of where you want the camshaft. (To check valves, try to push down on the rocker arms with your fingers...if in the right place both the front rockers will feel "loose" and you will be able to move them slightly. If one or the other is tight, then you probably aren't lined up right. Alternatively try to put a thin feeler gauge in between the rocker arm and the valve stem (the post coming up through the cylinder head). You should be able to insert a thin feeler gauge on both the intake and exhaust sides.
3. "Fine-tuning" adjustment of the camshaft (top pulley): There is a notch or groove on the camshaft gear. Here is where memory fails me...I don't remember if the groove will be right at the top and will line up with a groove at the top of the metal plate behind the gear, or if the groove should be right at the bottom lining up with a mark. I THINK the groove should be at the top...but if you followed the directions in step #2 it will be right where it lines up, or maybe just a little bit to the right or left. Align it exactly! Don't worry if it moves the distributor rotor a little bit away from the #1 spark plug connection...the whole point of step #2 was to get you "close" to where you needed to be, the notches are the real alignment.
4. "Fine-tuning" the crankshaft: Again I don't remember offhand the exact alignment. I THINK it will be a groove or notch on the crankshaft pulley (the bottom pulley) with a mark or post on the metal plate behind the gears. I am sure the mark or groove will in this point be 'up'. This should be simple to see what is what, but if it doesn't seem to be like I said then go out and buy the Haynes manual for exact instructions. Again, don't worry if you need to shift the crankcase pulley a few degrees one way or another, the important thing is to get it lined up with the notch or mark...step #1 was just to get you 'close'.
5. Installing the timing belt: 1st off, are you putting on a NEW timing belt? If not, go jail without passing Home, as a new timing belt should cost less than $20, and the labor to change it is so extensive that every time you take it off you should put a new one on. Going to use an old one anyway? Make sure you put it on so it goes in the same direction as it originally did. But whoever took it off didn't even mark or line things up, so you don't know which way this old belt turned anyway. So use a new one. And if you are a hard core 4wheeler like I used to be, use a white-out pen and draw an arrow on the new one once it's installed, pointing in the direction it turns. That way if you ever have an emergency field repair and have to reuse an old belt, there will be arrows on it showing the right way to put it back on.
6. Loosen and backoff the adjustment pulley. This is a small idler pulley located between the camshaft and crankshaft. There are a couple of nuts or bolts involved. One is on the pulley itself that locks it into position. Loosen that one. Then there is another nearby, that holds the adjustment slide and spring. Loosen that one two...move the idler pulley as far to the left (as viewing from the front) and temporarily lock it into place by tightening the adjustment bolt. Again memory fails so I may not be describing this exactly right, but the goal is to move the idler pulley as far to the left as possible, so it won't be in the way when putting on the new belt.
7. OK time to put on the belt. It's toothed, and the important thing is to have NO slack on the right side (as viewed from the front). The crankshaft will PULL down on the right side of the belt and make the camshaft move. If you have any slack on the right side your timing will not be right. I would start putting the belt on the camshaft gear, and then push it onto the crankshaft. Once you get it started it shouldn't be too tough to slide it all the way onto the pulleys. If it's right your alignments on both camshaft and crankshaft will be good, and there will be no slack on the right side. If the notches don't line up right take the belt off, reposition the pulleys where they should be, and try again.
8. OK, now you think you have it right. Loosent the idler gear so the spring pushes it against the left side of the belt. Put your wrench on the crankshaft and gently slowly rotate the crankshaft clockwise at least two full rotations. Stop after two rotations of the crankshaft and see if all the marks are lined up again. (Note that the two pulleys rotate at different speeds, so sometimes both marks line up, sometimes they are 180 degrees out of phase.) Look good? OK, time to tighten the bolt in the center of the idler gear to hold it in place. Gently tighten the other idler gear bolt too, the one that held it away when you were putting on the belt. Note these are small bolts: Do not use very much force on them or you will snap one or the other off!
9. Well, it should now be right. But to check things out, turn the crankshaft around another 2 or 4 times. Watch the piston, watch the distributor rotor. When you stop your piston should be ABOUT at top dead center. Your distributor rotor should be ABOUT spark plug wire #1. And the crankshaft and camshaft markings should be dead on lined up as detailed in earlier steps. Still good? OK to do the rest of the reassembly.
I'd like to hear if these instructions helped or not. You can drop me an email at firstname.lastname@example.org Good luck. I used to hardcore run Samurai's, and at one point owned 4 of them. I had trouble keeping them smog legal and then changed jobs so no longer get enough vacation to off-road, so I sold them. But I had over 250,000 on mine, and my kid had over 180,000 on his, by the time we got rid of them.
Here's a slightly different way to do it
That answer was pretty much the same way the haynes manual says to do it. But I've recently found another way which i feel is easier and more precise.
Now, I'm assuming that the fan shroud, clutch and pulley, and the timing belt cover have already been removed. If you can't get that far, you might want to consider going to a mechanic.
Since this question about a timing belt being removed without alignment, we'll skip to the next step after belt removal. To start, make sure the tensioner bolt and tensioner stud are no more than hand tight. In order to get proper belt tension, the cam pulley must be able to move freely. To do this you need to remove the valve cover and back out (not remove) the valve adjustment screws enough so they don't touch the cam lobes. Turn the cam pulley clockwise and align the timing mark with the "V" mark on the belt inside cover.
Turn the crankshaft timing belt pulley clockwise until the punch mark aligns with the arrow on the oil pump. With the cam and crank TB pulleys aligned with their respective marks, the crankshaft is in TDC on the #4 piston. Install the timing belt so there's no slack on the drive side (side opposite the tensioner). To remove any remaining slack, turn the crankshaft all the way around twice. Once slack is removed, tighten the tensioner stud first (7-8.5 lbs-ft) and then the tensioner bolt (17.5-21.5 lbs-ft), then confirm that the pulley marks are still aligned. Reinstall timing belt outside cover, crankshaft pulley, fan pulley, clutch, shroud and alternator belt.
Now it's time to adjust the valves and ignition timing. On the drivers side of the transmission bellhousing is a rubber plug. This is the timing check window. Visible through this hole you'll be able to see a "T" with a line underneath it on the flywheel. Turn the crankshaft clockwise until the line is even with the bottom of the notch in the check window. The engine is now TDC on #1 piston.
If distributor was not removed from housing, make a mark on the housing just below the #1 plug in the cap. Remove the cap and check that the rotor is in the #1 position. If the rotor is 180 degrees out, then rotate the crankshaft clockwise one full turn and align the mark in the check window again.
Now you can adjust the valves to the cold setting. In this position you can get piston 1 & 2 intake and 1 and 3 exhaust. Intake setting is .005-.007 in. and exhaust is .006-.008 in. Rotate crankshaft one full turn and do piston 3 & 4 intake and 2 & 4 exhaust.
Replace the valve cover and bring the engine up to normal operating temp. Turn the car off and remove the valve cover (again) and check the valve lash (use the check window to find TDC again). Hot intake setting is .009-.011in and exhaust is .010-.012in. Reinstall the valve cover for the last time and don't forget to put the timing check window plug back in. Throw a timing light on that puppy and go have some fun.
Hope this helped someone,