Hondata says to do this to properly set idle.. (I am running S300 with a B18C type R engine)
"To adjust the idle speed:


1. Warm up the engine.

2. Set the idle speed to 850 rpm and move the duty cycle adjustment to the middle.

3. Unplug the idle valve.

4. Adjust the bypass screw until the engine runs at 450 rpm. If you can not reduce the idle to 450 rpm, then you have an air leak. Fix this before proceeding. If the engine will not run with the idle valve disconnected then your bypass port is clogged. Fix this before proceeding.

5. Plug the idle valve back in.

6. Clear the idle valve error. You should now get a smooth idle at 850 rpm.

7. Increase the engine speed to 2500 - 3000 rpm and abruptly let off the throttle. If the engine speed dips below 850 rpm, move the duty cycle slider to the right. If the engine speed hangs above 850rpm for some time, move the duty cycle slider to left.


Some engines prefer 900 or 950 rpm idle speed."

I tried doing it because I am having some idle problems and I want to restart the right way. Has anybody done this before?
For some reason I could not get my idle to drop below 550 RPM without the IACV plugged in and with the bypass screw all the way tight. I felt like I was going to strip the screw if I tightened it anymore.

Another strange thing was that my bypass screw was coated with some gray paint maybe, which flaked off when I went to adjust it to reveal the bronze that it should be. Was anyone else's not bronze at first?
What exact air leaks could they be talking about, if I can't get my idle to around 450 RPM in step 4?

 

IMO that specified 450rpm is a bit low. A steady 550rpm with the IACV unplugged should be good enough. That is the base idle for most Honda's anyway. Check your under hood labels to see what your base idle should be. If your issue is that your idle is surging/hunting. Then you more than likely have a vacuum leak that you will need to fix prior to setting the base idle.

If you want to go by the book you could check and see if the throttle plate is stuck open or could be adjusted a little tighter to reduce the idle as well. However, adjusting the throttle stop screw isn't recommended if you have no idea what it's for.

Yes a lot of stock Honda throttle bodies come with that silicone coating over the idle set screw. It's supposed to keep the everyday person from making improper idle adjustments.

 

Well my problem was that on hot days when I went to stop or slow down (put in neutral and let it coast) the RPMs would go down so much the car would almost die, and sometimes did. It was sporadic though. So I did all of the above but only getting the base idle 550 RPM and I think I fixed that problem. I only drove it today and it didn't do it.

The weird things: my car was fine for over 2 years touching nothing having to do with my tune or idle, and the problem described above started randomly so I thought maybe my IACV was going bad. Now, my idle is not perfect... when I let off the accelerator for it coast it drops below normal idle (850-900) for a second then hangs above 1k until I completely stops then it even takes another few seconds to go back to normal.

Then it looks like I was the first person ever to adjust the base idle since the engine was built by Honda in 96. Wow, I feel like crap now. I feel like therefore, I shouldn't have had to mess with it that way.

 

As things get older they wear and/or can get extremely dirty. If you don't keep everything as clean as it was new, the electronic idle system can be thrown out of line and require a mechanical adjustment. Or you can do a complete tear down and cleaning of the throttle body, intake air system (IACV/EGR/FITV...) and intake manifold.

 

True.. Maybe one day I will the IACV (I don't believe ITR engines or any OBD2 engines have a FITV) and the EGR is the black box breather chamber right?

Also, does my previous problem sound like an IACV issue to you? "on hot days when I went to stop or slow down (put in neutral and let it coast) the RPMs would go down so much the car would almost die, and sometimes did. It was sporadic though."

 

Most of the OBD2 engines I have worked on except the ITR has a FITV or at least an air rotary valve. It is a combination of IACV & FITV of sorts. The ITR may not have EGR ether, it is a diaphragm valve on the intake manifold for exhaust gases.... you may not have that ether. The black box breather chamber is for the PCV if I'm not mistaken.

Sounds like a vacuum leak or your tune might be a bit off. Could be your idle fuel trims or decelerating fuel cut off adjustments in your tune. I would double check for a broken vacuum hose or a leaking seal/gasket before you do any tuning adjustments though.