I had roughly the same problem after my recent re-build..... Mine would idle OK but when I'd get on the throttle it would start to splutter. I had air bubbles in the line between the filter and pump so I figured fuel filter.... changed the filter twice.... still didn't fix it. Eventually I ended up pulling the supply line off at the tank and gave it a couple quick shots of air right into the tank. That would fix the problem for about 50 miles and then it would start doing it again. Finally after about 3 times of doing that it cleared up for good, have about 3000 miles on it since then with no problems. From what I understand there's a screen over the feed line in the tank (although I can't say that with certainty as I've never actually had a tank apart, but seems I remember reading it somewhere), and my guess is it got clogged as it sat for quite awhile. A couple things that worried me about doing it that way was that giving it air like that might rupture the tank or make the sending unit leak..... made sure I had the fuel cap off when I did it..... and the other was that I might blow that screen completely off....... if I did I can't say, but if so it hasn't caused me any problems up to this point. If you're worried about that though might try it from the front as Man53 says.
Final Report.
First of all, thanks guys, your posts were all thought provokers, and all pointed in the right direction.
Looks like the whole thing boiled down to priming. I did just about every check you guys suggested, including blowing the lines backwards (disconnected the hoses from the tank and routed them into a clear food container so I could see what came out; nothing but clean fuel). I dropped the tank, looked inside, pulled the screen, it was (mostly) clean as a whistle. Flushed the tank, touched up some of the rust hiding on the *top* of the tank, back in place.
I also plugged the feed line at the tank side and fired up the Mighty-Vac into the fuel hose going into the pump. Held vacuum very well, so no leaks. Now WTF?!?
All that was left was air in various places: the pump, the filter, the tank line. So I primed. Held the filter-to-pump line up and dripped fuel into it until the line filled, and stayed filled. (This took awhile; that pump can pack in more fuel than I expected, so much so that I started looking on the floor for "excess". Hopefully, it was sneaking out the return line and back to the tank.) Before I reconnected the pump, I poured fuel into the top banjo hole above the filter until it topped off. I expected to *not* be able to top it off, given the fuel would follow gravity back to the tank, but after awhile it did top off. Go figure.
Buttoned everything up, said a quick prayer to St. Jude, patron of lost causes, and turned the key. Immediate, laid back idle. Stayed that way for 15+ min. Now it's time to drive it around the block, then 2, then 4, etc, etc, to check the *other* stuff I did. So much for the scenic route to a vary basic problem I could have nipped in the bud.
So let that be a lesson to me; moral of the story, if one depends on suckage to get fuel through a 6+ foot soda straw, uphill, air is the enemy...