Not particularly helpful I should say up front but... I've just restored my 400/4 and this included a Yoshi big bore kit, yoshi advise rejetting to suit, but don't suggest how much. I had a look at the this site and the US site, and there was rather more advice on the US one as one would expect with rather more people racing etc. An unscientific review of the advice was that for sea level use an 85 main jet was about right, and all the rest of the carb settings remain as standard. so that's what I've done. I've just given it the first service, bearing in mind I'm up to 7000 rpm steadily, with excursions to 8000, and plugs look to me to be on the slightly rich side, so I'll stick with 85 for present. Otherwise the bike runs really well with clean carburation from tickover upwards.
Main jet really only affects mixture at large throttle openings, so I might suspect that you've got some other thing going on if it won't run at all. Perhaps somebody better versed on here may be able to help?
Arfa.