Mike, you are doing great. It feels daunting at first, but the feel and your own style show up with hands-on time. You are not going to ruin anything and by working through it step by step, and maybe having to do a step or two over again, you'll learn a ton, have a better understanding of why it acts the way it does when you're driving around. Most folks never try this at home, so respect for jumping in.
I want to lay out the approach I am using. I picked it up from Leech Motorsports and it lines up with what you are doing. If you see anything that conflicts with what you are learning, I'd love the feedback. I'm definitely still a padawan regurgitating from the masters and having only had my hands on 3 cars.
The big win on Black Jack has been a working IAC with the stock computer. Grover did/does not have one since I got it. Father Time lost the BS3's IAC channel when I added driveshaft speed to gain slew rate control. On those two cars I stabilized idle with a higher RPM & timing only. We can get into that if it becomes relevant. For now, using the IAC to get a steady idle just works better. The stock computer can also preemptively bump airflow when the A/C turns on to keep things steady and handle similar loads.
The best idle comes from getting the base RPM & IAC DC right. Set the base, with IAC unplugged, fixed timing, & in open loop and at full temperature, so the engine barely idles, then plug the IAC in and look for about 100 to 150 rpm more with an IAC CD of 20-35%. That gives the IAC room to add air and also to pull a bit if it overshoots. I needs authority both ways. On mine I ended up near 30 percent and that sits in the window.
My steps. I lock timing at about 20 degrees using the computer instead of pulling the SPOUT. I unplug the IAC. I let the engine warm up fully and make sure it is in open loop. I set the throttle stop so the blade is almost closed and the engine will just barely run. Stumbling & stuttering is fine, so long as the engine doesn't surge or die. I note that rpm, then set the ECU target about 100 to 150 rpm higher. I plug the IAC back in hot and check that duty falls in the 20 to 35 percent range. There's some MAF settings & airflow expectations in the stock computer that I don't think are relevant to your MS.
Next, I work the commanded AFR and match it real O2 results by adjusting the VE table, as needed. I keep the idle cells smooth so I am not chasing steps. Picking the exact AFR is part art and part preference. With a healthier cam I usually land north of 13.5 to 1 for a clean idle. With a more mild cam you can go quite a bit leaner. I've been over 15:1, but honestly without cats, that's pretty eye-watering. If it chops at lean targets, give it what it likes and move on.
Once fueling and airflow are steady, I open the timing tables and let the computer assist idle stability with timing. Shape a small spark mound around idle so timing increases a few degrees below target RPM or at slightly higher MAP, and decreases above the target RPM or at slightly lower MAP. Avoid cliffs that make the ECU hunt in and out of the target. If you give it too much authority on air or timing you can create surging, so keep the corrections modest @ not more than a 2* delta between cells.
Two last notes. You are speed density here, not MAF, so smoothing the VE pad around idle matters. Also watch battery voltage at idle. Poor voltage control can look like a tuning issue.
Once you have a glass smooth idle, try a little more timing and see if it will accept a touch leaner AFR. You can bring the rpm down a bit too.
I hope you are having fun with it. I am having fun tagging along, getting a refresher as you work through the steps, and it is pushing me to get back into the tunes on my cars.