Finally Started up my Project...A few Questions.

2 turns out on the pilot air screws is good and yes most impact is on the idle circuit.
Air box is good
Earlier you said fuel level was right . (Having the correct fuel height has a huge effect) so that sounds good
When you had carbs apart you would have noticed if there holes in the diaphragms . Right now I can't think what else might prevent being able to rev. Twisting the throttle opens the throttle butterflies/flaps allowing the cylinders to pull in more air and gas.
Blocked primary or secondary main jets would have been easy to spot while cleaning carbs so that's unlikely
Perhaps it is the exhaust leak?

I checked the diaphragms closely for any tears, so I think that is fine.

It may have something to do with that exhaust leak, but I have a feeling I just didn't let it warm up long enough. My wife has a dirt bike that does the same thing (little response when you twist the throttle until it is good and warm). The symptoms feel the same as that.

I will let it have a good warm up and see what's what.

After being away for a few months, I am back at my project bike.

It will start up with no problems, but it does not seem to be running on all cylinders. Like before, #3 is not firing and I think #2 has an issue as well.

I have two sets of coils (original and Dyna), and the issue occurs with both sets (each have their own wires as well). When I do the spark test (just by holding the plug against the engine), I get a nice looking spark on all of the plugs.

As I mentioned earlier, the compression and valve clearances are fine. When I did the valves, I counted the links on the chain and that was fine. Is it possible that the timing can still be off even if the cams are set up properly?

If it isn't the electrics, then it must be the fuel. I have cleaned the carbs, but I will pull them off again and soak them for a few days to ensure that all the passages are clear. I have already checked the float level using the clear tube method, but I will do it again.

Any other suggestions?

Thanks for your time.