Flashing Check Engine!!!

When the misfire happens above 1000 for a prolonged period the light will blink like crazy. I had misfire in #3 below 1000rpm, and misfire in #6 above 1000. Various things: Your compression is way too low, bent valves(which will destroy the guide and kill head...personal exp.), or bad coil. It can become a more serious problem. Disconnect the fuel injector when you drive it so you don't keep dumping fuel in there, washing it out. Don't punch it. Drive nice.
I've learned thru experience with both chargers and juice.....my 2003 GT I've had since Jan has had two whole motors put in.....both were beyond rebuild.

you can go with some choke stuff/carb cleaner around the intake around #5 and see if you have a leak anywhere.

I think that it would indicate a misfire from low compression. I didn't realise you said that it was a low comp short block. I just read a threat somewhere earlier about low compression causing the light to trigger. I think it was a write-up about the problem with using cam regrinds with mod motors.