*PRO TIP*
Use an angled screwdriver on the brass screws on the IACV/ISCV.

Heh, I already cut those off (or turned them into flatheads) and replaced with hex nuts. I'll probably be doing the same for the motor.

Way to be a typical male.

You can hook the ISCV directly to your car battery to spin the motor fully open/close. Helps in the cleaning/lubing process.

I didn't have my impact driver handy!

>
That's what I did also.
When I put a Beams into my Rav4 the IAC was bad. We tried cleaning but no good. We got one from a 05 Echo IIRC that was a perfect match.

I'll keep that in mind. Cleaned it again though (and removed the motor to clean that portion) and the idle is greatly improved. Now down to 900-1000, or at least near the realm that my gauge could be off (I'll double check with OBD2). So, this is good.

Had one quick instance where I revved it this morning and it acted like it misfired and sort of skipped a beat and briefly flashed the CEL. No stored code though. Not sure if it could be bad gas or what. My coils looked fine yesterday.

At least the idle is improved! I doubt if you have bad gas, or your 5S would've been having problems too. When I first fired up my BEAMS, I had a snipped COP wire going to my #3 cylinder. It never threw a CEL despite the fact that I had one cylinder that wasn't firing at all. It's weird that you're getting a CEL without having a stored code... Is it stumbling pretty hard or does it act more like it's barely missing? I can't imagine the coolant temp sensor could cause it to misfire, so we'll rule that out. Same goes for the TPS, it will affect the engine some but won't cause any major issues. Crank and cam position sensors are working great or else you couldn't even get the motor started. For it to stumble or misfire, I'd say the biggest factors would be the MAF or the COP's. Could have possibly skipped a tooth on the timing belt but again, not likely or you'd have more problems than a random misfire. VVTi solenoid won't cause a misfire either, just sluggishness.

Running wise, it seems to have improved. I drove ~100 miles today with no running issues except...

Cooling. The temp sensor is really jumpy, and it doesn't seem as though the system is getting pressurized. So I'll check that. It seems to do fine temperature wise, and then jump around every so often. Leads me to think maybe radiator or something - which I should probably replace anyway since mine is pretty old and non-OEM.

Maybe air in the system? Jack the car up in the front or park it with the nose up, remove the radiator cap and let it idle a while. Don't do it with a warm engine though, but i don't think i have to tell you that

Probable you've already tried the above, but sometimes people just forget about it