Will a Yamaha xs400 engine replace a xs250 motor?

Answer 1

In a word, yes.

The only difference between 250 and 400 engines is the top end, so you just need to replace the pistons & cylinder head etc. As far as I know the crankshaft is the same.

Hi, crank actually has a different part number, probably, (and this is a guess) the balance factor will be different as the pistons wont weigh the same as a 250's. Don't forget top end includes carbs ;-)