Dude....it doesnt matter if it's vtec or non vtec...a vtec jumper harness and a non vtec jumper harness are the same...no matter what, the wires for vtec are gonna be there.
And if you're gonna replace your harness, use the same goddamn year...fuckin' A, man...common fucking sense!
If you don't know simple details like that, you probably shouldnt be fucking with your motor by yourself...
But at any rate, here's what you need to do:
1. Buy a 99 EX 5spd wiring harness. Just the under-hood harness. And it HAS to be from a 5spd. Don't come back in here with 'my buddy with the white RX-7 with the Golden Gate Bridge on the deck lid said an automatic harness will work' because it WON'T. Got it? GET A FUCKING 99-00 EX MANUAL TRANSMISSION ENGINE HARNESS .
2. Buy an obd2b-obd1 jumper and an obd1 LS ecu.
3. Plug the 99-00 EX harness onto the LS motor. You'll have a few wires left over for VTEC, VTEC oil psi, and the knock sensor, but don't worry about it. THIS WILL NOT AFFECT ANYTHING. Got it? IT'LL BE OK. You follow me?
4. Inside the car, plug the green plug from the engine harness onto the green plug inside the car. Plug the obd2b-obd1 jumper into the harness, and plug the obd1 LS ecu into that harness.
This should be EVERYTHING you need to do, if in fact the motor is in the car correctly (mount-wise and whatnot). Like I said, you will have a few wires left over but DON'T FUCKING WORRY ABOUT IT. YOU ARE NOT USING VTEC, THE ECU WILL NOT BE LOOKING FOR VTEC SENSORS, AND YOU WILL NOT THROW ANY CEL'S.
And you could have fucking searched and found everything I just wrote. Fucking lazy ass n00b.