The pistons are 90.3mm.
They make kits up to 1010 on the stock cylinders, so this leaves much more wall thickness than those do. Like my dad said, we've not had any problems related to the big bore. We burned one piston on the triple, because we were running it too lean with too much compression. If anything, we could use a little more timing on ours on the top end, so I'd think you would be fine there. We run the 6 post clutches on all of ours, and we also run the harmonic balance ring on them. Don't know that we really need to, but it dampens the vibration significantly.
On the EFI, you'd need to run any fuel control box. We run ours with aftermarket single pipes, and they work well, I'd think it would work quite well with the stock pipe as well, although not quite as much power.