Apparently my misfiring and throttle problems are not ignition related. Spent all weekend on troubleshooting, and realized I have several different problems.
1) I believe my fuel pump is failing. The relay is fine, and I replaced the fuel filter. I get periodic misses while driving, and I'm starting to hear different noises from the fuel pump
2) The multiple firmware and software changes for the Hydra have royally screwed up my tune, and rolling back to r68 and my original dyno tune have 'solved' my huge throttle tip-in problem. I'm going to have to work with FM to figure out what all changed, so I can at least get the base settings right on the latest firmware. Their latest base map won't let the engine start, but then it's not set up to account for my various changes.
3) The Fab9 ignition upgrade seems a bit suboptimal for installation on an MSM at the moment. I could only get the car to fire with it in with a lot of trouble and lots of cranking, and only when hooked up to my wife's 2 with jumper cables. Once it is running, it sounds fine initially, but gets rougher and rougher as the engine heats up, struggles to maintain idle until it finally stalls. I'm fairly certain that the core of the problem is in a weak connection between the plugs and the coils, specifically because of the MSM's tighter valve cover on plugs 1 and 3. Plugs WAY fouled from flooding the engine multiple times doesn't help.
Some pics:
A really good quality kit.
Looks pretty good installed in the valve cover (they were still too high in this pic), though the wiring is rather messy at the back, in part due to where i mounted the coil driver.
The coil driver was designed to be bolted to the coil location for the pre 2001 cars, and can be bolted to the firewall instead. But we don't have room for anywhere that I could get a drill. I'd have to start pulling out a lot of other stuff to get a drill to the firewall in any of the available spots I could find. And no option at the back of the valve cover. So I used a bolt and nut and that mystery bracket hanging off the brake booster
And how jacked up my new plugs became from all the flooding/no-start. Literally brand new plugs from the first pic, after about 15 minutes total of engine running and several dozen start attempts.
I'm going to re-install the ignition today (with clean plugs), on the old Hydra map and firmware, to see if there is any improvement there. Discussing with Fab9 options for confirming a solid seat on the plugs.