That's not to mention that while stuff like the transaxle and the like is out, its a REALLY GOOD idea to go ahead and replace any potential wear parts-and there will likely be enough that are close or over due if you're talking a 15+ year old car. Even though it's a big initial cost, stuff like engine mounts, front end bushings/joints, CV joints, belts, hoses, and the other things I'm sure I'm forgetting are a LOT easier to change at this point, and you could be looking at $1K+ in parts. If the car is a manual, it's a good time to change the clutch-again unless it's brand new(20K miles or so) it's a whole heck of a lot easier to get to at this point than it is down the road. Even so, it's a lot cheaper to do it upfront than have to do it with the engine in the car.
It's sort of like when my dad had the head changed on his truck, I virtually forced him to buy a new timing belt and water pump on the philosophy that if the old one has to be removed anyway, it should be replaced with a new one.
Yeah that's a great point. If you're already in there there's a lot of stuff you "might as well do" since the car is taken apart... assuming the swapped engine isn't practically brand new.
It's one of those things- like you're doing the water pump so you might as well do the timing belt, or the timing belt is due for a change, so you might as well due the water pump. If you're in there, there's not sense in waiting for catastrophic failure.