Prime suspects for me are your petcock and fuel filter.
Make sure you have a clean OEM fuel filter. I ran a brand new generic filter once and found it wasn't allowing sufficient flow which caused my bike to run crappy. I swapped it for a new OEM filter and problem was resolved.
As for the petcock, I've had problems with them on two separate bikes and both times they were pesky, finicky symptoms that drove me nuts. Can't hurt to rebuild it (or swap out the entire unit if you're willing to part with the cash).
Sounds like you're close to nailing it down, good luck.
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When you see me, it's already too late.
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