The culprit was the new spark plug 104s. I put Motorcraft 447 and set the gap at .05 and running much better now.
After troubleshooting with the laser thermometer I found that the cylinders temps would fluctuate a lot and I had to take reading in the exact same spot on the header on each one.
I think this is what Dirtdonk was getting at with imperfect parts etc.
It took Broncobowshers advice again and swapped plug around and noticed one cylinder would run a little cooler with one plug. Went out and got new plugs and running much smoother!
Still got some dialing in to do and I think I'll have the distributor curve redone for tourque, but so glad its running better.
Going to put some miles on it and play with idle mixture and timing some then check spark plug health.
Thanks everyone for all the advice!