Just an update: After a few hours of troubleshooting at a good bike shop they concluded that the ECU was bad. They tried changing a few different parts with another S1000RR 2010 until eventually swapping the entire ECU.
Bike started 10 out of 10 times with the other ECU but as soon as they switched back to my old ECU it didnt start.
They are not sure what broke it, perhaps me boosting the bike/battery several times burnt it. They did find cables from an old PCV still "half connected" which could also be the bad guy here. Only error codes they could see from the old ECU were "low voltage" and "high voltage".
Anyway, they will swap ECU and hopefully the issue wont come back.
Been thinking of swapping the cable harness just for good measure...
Thanks everyone for the feedback/tips!