Ah, that is a very very big problem.
You cannot interchange the engines you have described like that. 1995 is OBDI, and 2000 is OBDII. Completely different electronic architecture.
The absolute best you can do is pull everything down to the "long block" and swap all the components - every last one, every sensor, everything on the engine. Then you may have a shot. But it's still a guess as to whether or not it will work.
Sorry...and best of luck.
I'm sorry to be the guy to say it! But like I said, all is not lost -- you could likely use the block and head as is. I would change everything else, from injectors, to intake, to harnesses...all the way. I think any block or head differences would be insignificant to the difference in sensors and engine management. So all is not lost...