I would just lend this advice. Disassemble the motor, get a degree wheel on and interpret all the vital info. Then look at the pipes, carbs, stinger diameter, squish configuration, carb flange design etc. All are important to a happy motor. I can not say which ignition is "better" but I can say the old 3 pulse stuff works just fine.
Why do you soften compression in 1000'? C-16 seems adequate to handle up to 16:1 in 1000' I would think. Did you dyno test any different fuels? C-14 or 14 plus? Who completed the case porting for this motor? Many variables to consider, but most certainly this motor should be stronger than the dyno numbers from Iantommasi's. And I know they have made many dyno laps, and have also built many strong strokers such as Benji's. Did they offer any advice or input? Good luck.
Pro Stock 1000 #10x Falmouth, Maine
2008 NSA Champion
2008 Wahl Cup Winner