I bought a 98 Civic ex coupe manual that has a D16Y8 from a 00 automatic in it from my neighbor. For the most part I've got the car running proper again. My last hiccups are a constant p1508 (IACV) and a sporadic p1106 (BPS). My understanding is that the BPS is in the ECU and can not be replaced without replacing the ECU. The problem is is that I don't know which ECU to go with. I've read quite a bit on the forums and I'm not satisfied with what I've found so I figured that I would ask.
What I've read is that the distributor from the 98 should have been used and the ECU from the 00 should have been used. That raises another question for me, if that's even true. Would I need to get an ECU from a 00 manual and not a 00 automatic. Apologies for being so long winded I just wanted to include as many details as possible.

 

98 car, use 98 stuff to make things easier on yourself.

98 Dist:
30100-P2F-A01
30100-P2F-A02

98 ECU:
37820-P2P-A34
37820-P2P-A84

To save you more headaches, try to find a complete 96-98 EX MT intake manifold as well complete with throttle body, injectors, sensors and solenoids.

 

This is ALMOST correct...
The '98 distributor makes your life easy since you have a '98 Civic EX manual engine harness. If you use the '00 distributor, you will have to change the engine harness plug to match it or purchase an adapter for a plug-n-play solution.
No ECU change is necessary... the ECU you have in the car originally would be just fine. Remember that you do not need an automatic ECU just because you have an auto engine... you have a manual transmission in your car now, so you must keep a manual ECU or you will get automatic related codes that cannot be defeated.

Where the OP and feriohhh have missed the mark is a '00 manual intake manifold will be required to swap out with the auto manifold on the donor engine from your neighbor. This will solve the 2-wire IACV/3-wire IACV dilemma and make sealing the intake manifold easy so vacuum leaks don't give you fits. The '98 I/M is a bear to make work on the newer cylinder head. You can block off the fast idle cooling port sticking straight up in the middle of the I/M mounting flange with a vacuum cap and all will be well in the world. Good luck.

 

OP, did you have the Baro code before you swapped the engine ?