Just a wild guess, but did you bleed all the lines or just a few? On my old 3 cyl Ford, when I run it our of fuel, I can get it started if I bleed just one line, but it runs rough and has no or very little throttle response. Bleed the other two lines, and I usually have to bleed the lines twice, and it will crank and run fine.
Moral of story- bleed all the lines 2 times.
