One of the common problems with a miss at higher rpms is the vent hose in the right air filter bottoming out. Since your filters are shot this may well be the actual cause of the miss at higher rpms too.
Check the vent hose and make sure it is seated properly and the tip is cut at a 45 degree angle.
With new filters and the vent hose getting proper air flow the miss should disappear. You will most likely want to adjust the air mix screws back down to about 2 3/4 with the new filters too. 3 and a half is usually a bit much with stock.
Patriot Guard Rider
2000 VN750 Sere (Serendipity)
1990 GL1500 (Ole Blue)
1986 VN750 EVie (project bike, heavy custom)
VROC # 11628 / 25000-H
ARVROC # 12 Coordinator and Crowd Control
OKVROC # 18 (H)
TNVROC # 45 (H)