my buddys dune ported 350 was breaking up in the higher rpms and it ended up being the flywheel!
Just something else to consider.
I dont think you are running out of fuel but if you are you could always put a fuel pump on it.
Get one off of a twin cylinder snowmobile and plum her in.
Also make sure your floats are set right, check to make sure the needle and seats are clean and not sticky.
You could also gut the stock gas cap, drill the vent line hole bigger, and de screen the stock fuel valve and drill the hole in that bigger.
Make sure you are using big enough fuel line, and that the tee in the line is not restrictive.
Dont count out electrical components also. A bad stator or coil can cause a high rpm miss also!