Being near sea level then, you may need to richen up your main jets a size or three.
But for now you can test things with different tuning methods. Changes in timing, changes in idle mixtures, changes in anything that's old (maybe the plugs need cleaning and gapping?) and stuff like that. All simple adjustments.
But headers and dual exhausts are well known for making an overall mixture a little leaner at the intake end. Putting a lot more pressure on the ignition/spark than normal. So a stronger ignition is a must at least (which you already have with the Pertronix), and re-gapping plugs can actually make a big difference.
But in the end, you may just need to richen up the mix a bit with larger main jets.
However, almost up there with cylinder heads, doing main jets would be near the end of my list even if I thought it was the most likely. Nothing wrong with making sure things like vacuum leaks and ignition tweaks are done first. Not like changing jets is the end of the world of course. Just takes a bit more hassling around than the other stuff.
Paul