All of your jets will effect "Overall fuel" in the system. So, more pilot fuel will carry over to the high speed section.
Since you cant get from mid, to high RPM... that means you need more fuel in the pilot system. Basically, since you can't get into your "High" speed system.... there is no reason to change the high speed jets. (yet) When you tune a carb, there is no fast way to do it. You will need to have them a part a few times, and you don't want to change too much at one time. The nice thing with the high speed system, is that you can add more fuel with the high needle.
I can tell you right now that your dead spot is because of the filters, and not the new pipe. When you ask us for tuning help, you have to tell us EVERYTHING you have changed. I hate aftermarket filters as then can be a bastard to make run properly. Not to mention... if yo have the big plastic air box... it can support +130 HP without an issue.
As above... I wouldn't go too low on the pop-off, or you may have low RPM issues. BUT... I may get it between 20 to 22 psi.
Finally, when you get the carbs apart again... make sure that the check valve in front of the high speed jet is in good condition, and make sure that all the transition ports are clear. Use spray carb cleaner at the jet, and make sure you can see it coming out all the ports. Also, I would recommend using cleaner, and compressed air a few times just to make sure they are totally open.