Make sure all of the rod bearings are aligning properly. Sometimes a bearing will be slightly "canted" and it will rub against the crankshaft. Make sure the rods and pistons have the correct side forward.
As you reassemble make sure that each piston/rod combination is still moving somewhat freely. Turn the crank a few turns before going on to the next. Since the rings are not seated they will drag a little on the cylinder walls until the engine has run for a bit, but you should be able to take that into consideration.