I've had a similar problem, and mine also occurred shortly after having the oil sump and fuel nozzle mods done. Taking off from a sandbar on the Missouri River, my engine began running very rough at full power. As I pulled the power back the engine smoothed out and I headed into the nearest airport in Columbia,Mo. Enroute, the engine ran smoothly at less than about three quarters throttle, but would begin missing at higher power. After landing I had the airplane checked at the local maintenance shop, but they could not find any obvious problem. I called Stan and he agreed to overnight a spare carburetor to me, since we suspected the problem was related to installation of the new fuel nozzle. Prior to this, I had 700 hours of trouble free operation on the engine.
The next day, with the new carb installed, everything checked fine on the ground, but right after takeoff I had the same problem. I landed, taxied back to the local shop, left the airplane with them to trouble shoot, and rented a car to get home to St Louis. One week and several thousand dollars of trouble shooting later, the airplane was repaired by replacing the sparkplugs and ignition coils. It was apparently not related to the new fuel nozzle or oil sump. This happened just a few weeks ago, and I've flown about 20 hours since then with no further problems. My airplane is a 2010 model, so it sounds like I need to also check the separation of the sparkplug and ignition coil wires.