Sounds like you've got a pretty good idea of things, there's not much more to add lol but I'd recommend a quality marine grade bearing grease (lasts forever), a lil on the clutch drive gears (no more than a gob the size of a pencil eraser so it won't fling into the pads) and don't forget the lil ball bearing clutch actuator & pushrod uses. If you're planning on tearing down the motor a gasket set can't hurt - usually the head gasket is no problem if the engine hasn't been run (even if it has... usually) but a set is cheap enough and provides excellent templates for making your own out of quality materials. The base gasket in particular never likes to come off intact even with a new motor and you'll need one if ya wanna do this: http://motorbicycling.com/f13/basic-porting-16646.html
Even if ya don't wanna get that deep into it - I defo recommend port matching the intake and exhaust manifolds, the SBP mount flange is FAR better than stock, but it and the gasket could still use a touch.
I'd not recommend rubber mounting, while there's some polyurethane variants that'd work it entails welding etc... or an entirely different mounting system like Manic Mechanic offers (neither option will work w/a shiftkit BTW). There's been much debate on this topic ofc - but just putting something between the stock mount points and the bike's frame doesn't work out as it isolates the engine's vibration (not eliminates) and the mount fasteners tend to sheer.
If yer going shiftkit then much of the vibration will "disappear" anyway as it's usually from the rear sprocket not being perfectly centered (impossible with the kit one) and the tensioner and not so much the engine. I've not even bothered to get soft handgrips for my shiftkit ride 'cause I don't need 'em
Coupla tips 'bout the shiftkit tho if ya want 'em;
I took some pipe with the same inner diameter as my seatpost tube's outer diameter & cut it up to make steel "pads" to diffuse the crush/crimp of the pipe clamps (the "pads" and the clamps were later tack-welded);
(click to view)
and it's not really the "optional" modification to grind the tabs a bit on the clutch cover to reverse the fasteners so the nuts are accessible - if ya don't you'll hafta pull the shiftkit/engine every time ya wanna mess w/the clutch a bit... but it's an easy mod;