Driving around with my dual empi's. As I accelerate I hear what seems like misfires. Valves recently adjusted, timing and carb adjusment. It's usually worse when car is cooler and almost goes completely away when vehicle is at running temp but still can hear misfires or what I think is misfire. I checked exhaust but it seems ok. Any ideas?

I have a set and they work well. Sounds like your idle jets are plugged.

How can I fix this issue if idle jets are plugged?

Just pull them out, look through them in the light and see if you can see any crap. Blow them out with some air. I also take a can of carb cleaner and stick the red twiggy thing into the idle jet hole and blast it to knock anything out of there. The other problem with these carbs is the enricheners sticking open and you go full rich. JB weld them shut (down) from behind the steel plate.