main bearing failure right side 2006 ec300, rebuild tips needed.

[hillbilly]

Recently bought little used ec 300. UK based.
Third time out, trail riding, clouds of smoke and rumbling. Crept home ok, strip both sides and right side seal in bits and bearing worn with cage breaking up. no major damage luckily.
Is this common 300 fault, wouldn't expect this on 6 year old bike. Any design issues as with 99 bikes, I had one with mains issues, that was wrong bearing type and small oilways.
Not split yet to replace bearings. Working away at present.
Any tips before I start?
Read a lot here but have slight concerns as some mention crank alignment and main bearings not needing to be up to back face in crankcase. Think it's roller on right side (06 bike) so assume this not an issue, or is it?
Service manual states seal with lip outward, is this right? Mine destroyed and can't see. Not pulled flywheel yet to check left side.
Also some references to gearbox problems with these bikes, what should I be looking for when split?
Looking to keep cost down, any issues with buying off the shelf bearings and seals from local bearing suppliers. Someone said heavy duty bearings available, sounds sensible. Also references to different tolerances for higher temps, is this obvious from bearing markings?
Service manual states 'mark clutch basket before removing', didn't do that! What's that about?
Home in a week and want to be armed with as much info as poss before I start.
All comments appreciated.
cheers
Simon