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I just installed a used P13 JDM ECU tonight and the car runs alot better. The P28 with the Hondata S200 has been removed entirely . So now I have an H22 with an H23 intake manifold with stock Si VTEC injectors. With the other ECU my idle was high but steady at 1200 rpm. Now it bounces from 500 to 1200 when I come to a stop, and keeps going back and forth. My ex gf's car had this same issue and I don't think it ever got resolved. The car runs great otherwise! I am not getting 16 mpg I am getting closer to 30 again when I stick around 60-65 mph (I drove it over 100 miles tonight). I reset everything, unplugged the battery and started the car (not touch anything) and let it idle for 11 min.
So what could my bouncy idle be? What should I look for first?

Vacuum leaks.

ahhh this has happened to me twice on the same motor, and each time it was the IACV.
heres the 3 things that would cause it:
"-Fast air idle control valve needs cleaning. its located under the throttle body. theres two coolant lines that run to it if there clutter up like they tend to do it will cause it. or the part thats connected to the throttle body needs cleaning. (easy quick fix)
- Idle air control valve needs cleaning. its located on the front of ur intake manafold. theres a plus and two coolant lines and to i think 11mm bolts. take it completely out and clean the coolant lines and the metal screen that connets to the intake manafold. on mine my coolant lines was blocked. ( this is a easy easy fix)
- vacume leak. vacume hoses that are old or have cracks or a leak in the intake manafold or gasket i mean if its that then it will take u a while to find it. This is usually caused by mechanics working on ur car and not hooking back up a vacume line or pinching it. (this is a headake u can try to do it but it would take u along time unless u have good luck)" -honda tech

Yay I'll just start cleaning every bloody thing I can! Thanks!

Ok I took apart my IACV on the front of the intake manifold and it will full of a black gunk. I cleaned and sprayed it out. The car starts better my my idle is still about 500rpm on start up when stone cold. I then took apart the Fast Idle thingy under the throttle body. That had lots of white gunk in it too. I never found anything pluged up. Everything was just dirty on the inside. I used liquid gasket to seal everything back up. I checked a good number of the vacuum lines and I found faults with a few of them and I am going to get some tubing and replace them all and see what happens. Oh and both my little check valves that were inline with the vacuum lines were stuck. They move freely now.
My idle doesn't bounce anymore ^.^
I think my IACV might be faulty (cuz it was just full of that black gunk, nothing was fully plugged up though), I don't get a CEL though

it wouldn't throw a cell

IACV I would say was your idle bounce culprit. As far as low idle, even on start... Take a picture of you FITV taken apart.

Yeah something went wrong here for sure. Looks like the resistor inside there melted and then popped! I know how it happened. I can't believe I didn't look at it earlier! I had the IACV plugged into it (12 volts) and that poor little sensor only takes 5 volts to run it. The car started better after I switched the connections and thought nothing of it. I am going to get a new one tomorrow and see how it goes. I think my IAVC is just faulty. I am in the middle of replacing all of my vacuum lines.

Anyways I took a bunch of pictures of the Fast Idle thing under the Throttle Body. It looks to be ok. I cleaned it some more but there was nothing wrong that I could see with it.

Some more

I did not find evidence of cracks or if anything could be missing. The seal seems pretty good around the metal plunger with the spring to the white plastic housing.

Dude, go to 92lude.com and check out the IACV mod. I'll post a link for it. Do the mod, and it will take care of your idle. The only other thing it could be is one of the vacuum lines coming from the intake manifold, check those too. BUT MAKE SURE YOU STILL CLEAN EVERYTHING OUT BEFORE YOUR PUT IT BACK TOGETHER.

http://92lude.com/idle_air_control_bypass_mod.htm

Good luck.

Thats a Fast Idle Thermo Valve (FITV). The Idle Air Control Valve (IACV) is on the back of the manifold. And yes, I agree, do the mod. Although, it might be a little difficult to get it to idle in the cold for the first start up. Just hold the idle at 1500 manually for a second and itll be fine.

I tried something like this, I foil tape over the lower hole and it lowered my idle a little bit, by 200 rpm. And it's still idles funny. Like sometimes it'll be at 500 and stays there, and other times it'll be at 1000 and just stays there. I don't have school tomorrow so I'll work on it first thing friday! When schools over I am going to take out the intake mani and take it all apart and clean everything, lol.