Well, I figured that the extra 20 minutes to do option 2 (looking under valve cover as Dave recommended) was worth possibly detecting something. Nothing to report. Head bolts are intact and snug, and I could not see anything else that looked abnormal. Exterior of engine looked normal all over.
So, I pulled the ICV and shot it out with TB cleaner. Definitely yucky, the TB cleaner was coming out yellow on the other side lol. Anyway, I put it all together and started it up. It idled a lot better, a little rough and still seeking up and down a little, but it was not dying. So, I took it to the nearest onramp and ran it up to 7500RPM. Pulls like hell. Flogged it a little more as my wife and I drove to our house (just bought one, still fixing some stuff before we move). When I checked under the hood, all the coolant seemed to be there and there was no milk on the dipstick or under the oil cap. No white exhaust smoke that I could see from the driver's seat, either.
After watering and raking some leaves, we left. The idle was super rough and seeking, almost stalling. After ~15 seconds it calmed down and drove normally as we went to the grocery store. When we left the store, it was stalling at idle again. After 15-20 seconds of me sitting on the gas pedal it stayed running, but with that "dip" in idle when you push the clutch in and let the engine go down to idle. My assumption is that there is still more crud in the ICV that spread around after I cleaned out the exposed stuff. I am going to take the ICV with me to work tomorrow and hook it up to a 12V supply and clean it with the door fully rotated. Maybe I will even stick the business end of it into the ultrasonic bath with some isopropyl alcohol for 15 minutes.
My only other guess about the loud noise, if it was not exhaust stuff settling, would be the intake manifold cracking or something. I have had vacuum leaks before though, and they don't usually do this. The ICV has not been cleaned in probably 6 years, so I assume it is that. If not, then I'll get in there with some duct tape and a bike pump to look for leaks. At least all that crap under the TB is gone now, making it vastly easier to access all vacuum hoses.
Anyway, positive results so far. No weird noises, pulls hard, no more black smoke when I floor it at high RPM. I also tightened one of the fuel feed lines' clamps down by the chassis (where the return line connects to the chassis under the brake booster). It was loose enough that the hose could rotate VERY easily on the metal chassis hard line. I tightened it a bunch, and it can still rotate on there a little, but the raw gas smell that I sometimes had after parking is gone. I replaced those lines ~7 months ago when I got the engine the first time so maybe I forgot something (I also used a little silicone dielectric grease on the hard line since the hoses are a PITA to get on dry). I have a ton of high pressure fuel line left over, so maybe I will just replace both lines again this weekend and wipe off the silicone.
Question...what is the easiest way to bleed the pressure from the fuel system, without just pulling a hose and letting it all piss everywhere? I noticed that the feed / high pressure line was a littlesoft and squishy, and the return line was firm. Maybe I made a big oops and used vent hose for the feed line? Looks like I have some shit to check tomorrow lol.