In just straight cost, your best to get a FZR600 engine because your only expense is the engine. You don't have to do anything else.
The YZF600 engine will directly bolt into a FZR600 frame with zero modifications. But you need to swap the swingarm and rear rim to get the chain alignment correct. For this you only need to by some new swingarm pivot bearings and spend an hour with a dremel cut off wheel to make it fit. But there are more things to buy to get it to run. You need the wire harness, coils, TCI, carbs. These add up very quickly when you look at the cost. Plus you need to run either pod filters or you need a 95/96 YZF600 air box and any year YZF600 fuel tank as the air box will not fit under the FZR tank cover.
You can find cheap engines. You just need to look and snatch on when it comes up. The FZR engine is the cheapest option, but to me the YZF engine is the best. It is all a matter on how much you want to spend. And I would expect that any motor selling for $100 will not last very long. Most engines are going to run about $400-$800 before any shipping cost.
Some what finished: 1989 FZR600 Frankenstein
In Progress: 1988 FZR400, 1997 YZF750