The best route for you to go is to modify your 99 harness for an older style 94-97 OBDII ECU. Then you can junk most of the emissions crap that came on the 98-99 Sentras/G20s. NO NEED FOR THE 99 MANIFOLD HERE IS WHAT I'M TRYING TO GET AT!
You can use all of the sensors from your 99 to run with a 94-97 B14/P10 Ecu, and keep the 2000+ roller rocker manifold.
This is by far the easiest and cheapest way to go when swapping a roller rocker motor into a 99.
Swap the 99 intake manifold onto the roller rocker motor like recommended already. This is going to take a bit more time as the 99 intake manifold takes a bit of modification to fit on the 00+ engines (clearance issues with the throttle body, and coolant hose connections in the back don't quite line up), but you can sustain all the sensors and stock emissions crap from your 99. It can be done but it will be a bit more time consuming, and maybe even a bit more thinking to get through.
The reason I recommend option number 1 is because I hate the 98-99 sr20de emissions systems. They're a pain to work on and diagnose and they are over engineered, and unnecessary. Nissan made a big mistake with these engines, I think part of the reason they started producing the RR engine was to fix these issues. Good news is that it isn't very hard to fit a 94-97 ecu on a 98-99 sr20 car, a swap of a couple wires on the harness plug, and ripping out some unused emissions components and you're done!