Sorry for the updates in rapid fashion but I thought I would share my process.
I ended up re-flashing the custom firmware a few times after I have tried to restore a firmware supposedly for the BBS02B I found on this very same forum.
That firmware gave me error 30 and did not work.
Upon returning to the custom config tool I noticed that the tool said;
"Failed to read status from motor controller"
I spammed restore a few times and kept having it write to the controller until I did not see this error.
I then disabled the speed sensor, shift sensor and the temp sensors after which to my pleasant surprise - the motor now seems to deliver full power again. With the wheel against the wall it did not stutter and I've seen an output of around 900W on throttle before obviously stopping.
Tomorrow I'll once again come back to update and troubleshoot a bit further to see if I can narrow down what my problem was after testing if it actually does ride at full power again now in real world riding conditions.
Everything seems to be working flawlessly again.
I've turned the speed sensor option back on without any error to the functionality of the motor.
My conclusion is that the shift sensor option ticked on caused the stuttering / janky throttle & PAS.
Turning the shift sensor option back on reintroduces the problem.
It almost feels and sounds like when the phase wires on a hub motor are shorted out and you put throttle on.
I've solved the issue of the disabled shift sensor by putting it on a brake switch connector.
A bit of troubleshooting and Nils's firmware is working a treat.
I have two profiles set up for both road and offroad profiles, switching is easy via the light button.
Only time will tell how long my controller will last, but atleast its back from the dead and fully functional again, plus extra's to play around with.
Some info about my motor and controller:
BBS02B bought 2023 via AliExpress.
750W controller 48V, MCU; STC15F2K60S2
TLDR: Users flashing this firmware and experiencing throttle / pas problems should try disabling the shift sensor option, in my case, it solved my issue.