Well the plot thickens LOL - OK I wouldn't try that pickup either but your idea of switching the other is good.
Bypassing the filter a short time I'm sure didn't do anything, have you dumped the filter into something to check if its picking up any trash??
The Yamaha's do seem to have issues with the VST filter, as they mentioned on THT, you would be only one more of thousands. Frankly based on other THT posts that is probably the issue on the motor, sure sounds like all the others. I think they can be cleaned and see if the yami guys can help you re-use the O ring too - both filter and O ring are $30 ea. Do a search over there and on Florida sportsman - boating. I think FS gives better info.
We have to have the motor running though - I don't think you even have an anti syphon valve - the vent seems good - I would blow back through the fuel line, that will clear any debris on the pickup at least for awhile to check it. If the tank has that much stuff in it you should find stuff in the filter too.
first thing now would be do the VST and get it running on the 6 gal tank with no filter - that bulb might just have been bad though, I have never seen one suck flat though and its not the vent- not the anti syphon - at least we're elminating some stuff - down to pickup and filter on the boatside. I'll do a search on FS and see if I can come up with anything
Ok did the search - good grief they have filters - here is just one that a guy is doing himself and seems helpful - I just did a search for VST filter in boating forum and and bunch comes up - you should probably do it yourself as there is too much.
http://outdoorsbest.zeroforum.com/zerothread?id=788906