Matt,
I have been running the Fox 35 with a muffler in my OTS El Diablo for several years. It first, I was having funky runs, changed NVA's (Randy, ST), tanks (round plastic double clunk, tin pinch corner, straight V), fuels (5%N 29% C; 10%N 27% 50/50), props 10x6, 9x6 (APC, wood), muffler pressure. None of these had any solid impact.
When I built the ship I wanted to use the round tank as it seemed to be a clean install and would hold the amount of fuel I needed. This had the plumbing coming through a 3/4" hole in the firewall. I set the uniflow vent up in back of the engine block thinking it would be in a dead zone and reduce the upwind/downwind effects. Sometime last year I remembered some advice that was given at a GSCB stunt forum many years ago (by who I don't remember) to locate the uniflow on the circle inside side of the fuse about 3/16" off the fuse side and pointing directly into the free airflow stream.
I made up a small bracket out of strip brass to hold a piece of copper tubing about 3/4" and installed it under the rear engine bolt. Hooked up the uniflow line to this and instant success! I can now set the engine anyplace I want and it just holds the setting. I went back to the full RMS 10x6 prop, 7%N, 27% 50/50 fuel.
I was having similar issues with my OTS Ringmaster that has an OS Max 25 (steel/baffle, ST NVA, muffler) in it. It has the typical profile stub uniflow tank that has the uniflow vent coming out to the top of the tank on the V. After the success with the El D I made up a similar fitting to mount off the back mount bolt of the engine pointing straight into the airstream about 3/16" above the fuse profile. Again, instant success. Solid run, 9x6 RevUp prop, set it where you want no fluctuations. It seems that the profiles have turbulent air flow over the fuse side and with the standard uniflow vent location straight out of the tank get pressure fluctuation all over the map, give it a try on the profiles it is cheap to try and should help the run.
One last thought is if you intend on using the Fox NVA you can seal the threads between the NVA body and tension ring with a piece of fuel tubing, it really helps. Also make sure the NVA to the case is sealed, I use black silicone gasket sealant. One last thing for the Fox 35 stunt on a profile if you run it in a 4-2-4 is the stick in the bypass modification, this eliminates the outside corner burp. You can search this forum it has been detailed many times.
Best, DennisT