I would pull the engine from the airplane, and put it on a engine test stand and try running it there and see if it has problems or not. If it runs good on the test stand then you have a problem with the fuel tank or fuel tank locaction.
If the engine is still running poorly, look at the fuel line going to and from the remote needle valve, do you see little air bubbles in it or not? If it has excessive bubbles then it is either causing the fuel to bubble (like in a vapor lock situation) or it is sucking air in through the needle valve unit.
You can try a external remote needle valve unit, before you try cutting the OEM one loose from the engine to see if it works better or not.