what went wrong?

[viper11]

hi
I just got my charger running again with its new forged 440 twin turbo, (have a couple header gasket leaks to sort)
I have the ms1 v3 extra 29y4, I was tuning the car in my driveway in park with no load using autotune at different rpms to get my ballparks again (it was running last year and my msq is pretty close ) brought it upto about 4000rpm and the autotune was doing a good job of smoothing everything out and all of a sudden it started misfiring on one cylinder (completely dead) as i reduced the rpm it slowly caused it to stall
I tried to restart it to see if it would clear up but it wouldn't quite start, after cranking and cranking there was a huge backfire that was extremely loud
I let the car sit for a few minutes and tried again but I could barely get it started and keep it running. its misfiring, popping and clattering. I had a hell off a time getting it up the driveway into my shop, it sounds awful, not to metallic, but not all exhaust leak either.
it takes 20-30 seconds of turning over the get it to start and i can only keep it running for 2-3 seconds, all the header pipes feel warm indicating fuel and spark

where should I look for answers? it went from 1 dead cylinder to not running at all, what could cause this???
I will do a compression test first then pull the valve covers witch takes 3 hrs cause of all the piping
thanks for anyones input (I know this might not be the ms but someone may have an idea)
I will be testing the ms with my stim too
jason