I forgot to update this thread - took the bike to an experienced indie mechanic who did a proper test ride. And he thinks there's nothing wrong with it. This of course leads to the question of what I'm doing wrong with my gearchanges, but I don't think it's me. I've tried slow changes, fast changes, it doesn't matter, the gearbox is just notchy.
He's adjusted the chain, but now it seems tight because it's clicking as I push it round the garage. Sick of it all now!
Along with the gearbox and the fuelling (which is improved with my mods, but still not great in my opinion), I've pretty much had enough of it. Considering my options for a replacement.
From reading around, there's a majority of happy VFR VTEC owners, and then some who aren't happy with the gearbox or the fuelling. I'm in that minority unfortunately.