You are always going to get a few bubbles in the fuel line no matter how it is plumbed, I think you may have a problem elsewhere. If it's an older tank, the uniflow or pick up tube may be cracked. Your spray bar may have some crud in it and causing issues. one reason I always use a in line filter is because I think it give the crank case vacuum something to draw against and gives smoother flow from that point to the spray bar. You might want to try muffler pressure for a flight or three to see what happens if nothing else works, and cant the back end of the tank out if at all possible. Justa bit can help with fuel pick up, especially at the end of an engine run.
Type at you later,
Dan McEntee