2006 fe450 charging/battery issue help needed!

hi guys, my mates got an issue with his fe450, basically all was well until his main crank bearing went and had to have engine rebuilt, it put a hole in his stator case.
he got the bike back rebuilt but we quickly noticed it wasn't charging battery so battery being old we put a brand new one on and it would fire up but something drained it within 5-10 mins!
we removed cover and checked stator and couldn't see anything obvious but didn't test it with multimeter, the lights still work on the front of the bike but the rear brake light only has one little led lit up.
we went out riding today and to get him going again we had to bump it as the starter button there was no clicking or anything from starter the battery was that flat, tomorrow were going to strip it and check everything over but I can't stop thinking about that crank bearing and stator case damaged.
should I be looking to replace that part first and give it a crack.?
any help or advice would be great as this lads at whits end with just having to pay for a rebuild on the engine and a new battery and still won't start off button unless charged!

hi lads it gets worse today, we took the battery off and gave it a solid charge and made sure it held voltage at around 13v then put it back on the back to fire up and check what charging voltage it was getting.
we innitially kicked it over and ran it for 1-2 mins and voltage measured at battery was basically just what I was measuring from battery and nothing extra going in from bikes charging system, we had a spare rectifier off a ktm so plugged it in then this is where it got interesting, it wouldn't start off the starter button, no spinning or clicking or anything.
this was something new so we started checking all wires etc.
continuity of earth cable from batt to where it bolts onto engine at bottom of starter ok, live feed to starter relay ok, fuse removed and checked along with the 3 little wires.
I bridged the starter relay and starter spun over ok.
now wondering what else to do or check and if this fault could be the one related to the original charging issue.
desperate for any help or advice please guys, this husabergs causing the lad assorts of issues at the moment after having the engine rebuilt.
is there any more fuses or common areas where wires break etc?