Update:
I got the EBL Locker system installed. It wasn't hard at all to wire up and flash. Did a few runs and ran what is called "VE Learn" to help trim up the fuel curve. I was still having the same issue as before, but not nearly as bad. Problem was, it only cleared up to a point instead of tuning all the way out. So I went and did a 10 min drive and datalogged it. The EBL software lets you playback datalogs in real time through the software. Timing was good, wasn't jumping around all over like it was, knock counts were much much lower, and none at idle and cruise, just at high MAP (over 80 Kpa) and WOT pulls. So naturally I start thinking fuel again. Pressure checked out okay at idle, but I was wondering if the pump was keeping up. 13 psi shouldn't be hard for a TPI pump to maintain, but ya never know...
I have two sets of spare injectors that I've cleaned and kept just in case. I wanted to eliminate the injectors as a cause, and it was a free test, so I pulled out the 6 month old injectors and put in a set of GM/Rochester original equipment injectors instead. The 6 month old injectors were still shiny, the older ones were clean, but not as shiny, lol. I lubed up the o-rings and installed the older injectors. I found the issue. Bad injectors. What little knock I was still getting is all but gone, last knock count was under 80. I did more "VE Learn" rides and watched the computer pull back fuel that had been added in earlier runs. NO stumbles, NO knock, NO WOT bogging. The fuel curve looks a lot better now, I had a few cells that were up to 100%, which is not a good thing, now all the cells are back to more sane settings. Now that I have this issue (hopefully) worked out, I can start refining the tune, work on the spark and AE tables as I learn what the engine wants. On the last ride estimated MPG was around 28/29 at 65 in 4th. Not too bad. I'm just getting started with tuning, but I'd recommend this EBL for anyone that wants to keep a CFI motor and still have the option to tune the motor.