CRF450 Rebuild Cost / General Advice needed

Hi guys, hoping for a little advice, about this time last year i stripped down my 04 CRF 450 looking for a 'loud gearbox noise' that i was told about from the previous owner. After getting the whole engine apart i found the gearbox counter-shaft bearing had seized onto the shaft itself, (which looks like the only thing gone bad) now i'm looking to put it all back together. Does anyone know somewhere to buy some good instructions and what tools i'd need. I should also add that it's got a Cylinder works 511cc Big bore / stroker kit on it so wondering if getting a new piston for that is economical, i doesn't look in too bad of shape (not much carbon) but i don't know how many hours are on the bike. Is it common practice to replace all trans bearings / main bearings, Piston valves etc? I'm weighing up rebuilding this one or buying a second hand motor std bore for it if it works out cheaper?. I've never rebuilt an engine before so i'm in no rush to get it finished. I've never owned a 450 let alone a big bore and don't know whether it would even be ride-able for me (5"10 130lb) so putting back to stock bore might be an idea but will also mean i'd be buying a new crank piston and cylinder at the least, on top of gaskets trans bearings and other parts. I'd be mainly doing track with some trail riding here and there. I know you guys know a lot more about this sort of thing than me, so any advice would be greatly appreciated!
P.S will add pictures and such if it helps?
Thanks in advance.