IMHO;

If you haven't flown tune pipes, the engine can't be tuned until the tank is pressurized. Just like YS engines. Jett's muffler is a tuned pipe. As the engine reaches top rpm and has pressurized the tank for a minute, then tune the engine. Just realize that the next start, the engine isn't too lean. You have to wait that minute to reach rpm.
Other issues that I have had with remote needle valves; is the fuel nipples on the carb and needle valve might be sucking air. But that usually doesn't flood the engine. The engine goes lean. Also check carb throat set screw for air leaks. Make sure that the pressure nipples aren't leaking from the pipe to the tank.
Another thing that is done with tuned pipes and YS engines, is to duct tape the fuel tank. This helps eliminate the fuel tank from bellowing a lot from pressure changes and will give a more precise tune adjustment. It also helps to keep the tank from splitting.
But, in my humble opinion, you just aren't being patient enough for the tank to pressurize, adjusting the needle valve too soon, then the tank pressurizes, and floods it out because you thought it was tuned.
Once high speed needle valve is tuned, with tank still pressurized, adjust low end with the engine running at about 3000rpm. It will peak just as the high end. Once peaked, richen 200-500 rpm.