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Could be debris in your fuel tank. Take off the tank, drain it, pull out the petcock (take notes/draw pictures on how it comes apart for reasembly) and clean the filters (two of them, one is the main and the other is the reserve), rinse the tank out a couple of times with a bit of clean fuel. Reassemble. I've done both of my bikes and had a fair bit of rust and peeled paint in them. I didn't experience the symptoms you have had but I can see how the debris left in there and build up over time could cause fuel starvation/blockage.
Good luck!
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'06 Scrambler: De-AI'ed, De-Snorked, K&N, Dual entry airbox mod, TORS, 135mains, 40pilots, thrux needles, no shims
'07 Bonnie Blk: De-AI'ed, De-Snorked, K&N + NH Peashooters, 118mains, 40 pilots, one shim
'05 Tiger 955i: Pulled airbox plate
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