PROBLEM SOLVED:
Here's what was wrong....Still not sure what exactly changed, but it was a combo of things that caused my issue. I think it was mostly related to the exhaust leak, probably even a little bit when I had it dyno tuned. It got worse over time, causing the AFRs to continue to come down until I was running very rich. The timing was set too high. Maybe it was right for WOT, but for the type of driving I do, it was too advanced on the base at over 14*. Then, I tried to set the IAC steps and the idle stop screw up with the rich fuel and too much timing, and when I had it to where it would run between 0-10 IAC steps at idle, my idle wouldn't come down to below 900. I kept playing with it and got it to where it was completely fighting itself, backfiring, idle too fast, leaking exhaust, it was a mess.
Much like the IT guy always says at work, unplug and start over. I went back to the very beginning and started over with the engine setup menu, and the dist. at 0 lined up on TDC with the #1 cylinder. I set the idle up so the IAC's would be right at about 800. Once all that was done, then I started with 5* base advance on the dist. Which raised the idle speed, so I had to go back and dial all that in again. Once that was set, I started to drive it around, and it did better already.
Each time I'd set the timing, I'd check it with the light at idle and make sure it matched the computer's idea of what was happening. Then I'd lock the timing at 25* and verify it would stay there at several different rpm ranges to verify the computer was actually controlling the advance. Unlocked the timing and check it again to make sure it would advance with the different rpms.
From there, I gradually added in timing and readjusted the IAC and idle set screw until I couldn't get it to hold 800 and under 10 steps on the IAC. I figured that was enough base timing, so I went back a couple of degrees and ended up at about 9* for the base. Since the dist is locked and I can only get about 20* total advance out of it, that means that I'll be limited to about 30 total advance, but for a big block, I think that is enough...I rarely get over 2500 rpm. If I need more I'll have to look into an adjustable rotor or something so that I can get the trailing edge of the contact on the post at idle and the leading edge at my max advance. If I understand correctly, I can pick up maybe another 10* by doing that, but then that's it due to the locked out advance.
So far, it runs fine, starts and idles fine, no more backfiring or popping. Little gas smell, so I may be a bit rich, but I can play with the AFRs and keep checking plugs until I get that right. Seems a little sluggish in the middle of the MAP/RPM range, but much better than in was. I may just think that because I've been driving my other car more, and I forgot how much a 37" tire will take away from your acceleration. Thank you all for the help, hopefully this will help someone else. I'll post my AFR settings and spark settings when I get them dialed in so anyone else can use them as a starting point.