How hard would this swap be? Will it bolt in? Are the electronics going to be an issue? Any tips? suggestions?

Electronics and sensors won't match up at all, the 99 is an OBD II motor, 95 is OBD I. A royal PITA if you ask me...you need a V6 from 92-95 Trooper/Rodeo/Amigo for the easiest swap. The easy swap groups are 92-95, 96-97, and 98+ (non-DI).

Def not the answer I was hoping for. Oh well.

I have a 2000 rodeo at work as a yard rig (junk yard) and its "fly by wire" meaning you would have to use the pedals and wiring to make it work. I wouldnt even know where to start, but then again im a toyota guy.

Yeah, that's even a worse PITA than the 99 donor, at least the 99s were cable throttle control.

I don't know why you couldnt just use the block & heads, IE switch your intake manifold and whatever other sensors are original to your rig, onto the later longblock