2011 Countryman S All4

I recently replaced the alternator Andy the problems started.
Hard start, rough idle, constant misfires(all cylinders), limp mode, CEL sometimes flashing, and the codes won’t clear

i have since replaced all plugs and coils, both cam position sensors, exhaust side vanos solenoid(intake side bench tested fine) and the timing chain and guides were replaced in February by a certified mechanic.

What should I check next?

 

Could it be a problem with the computer itself? My experience with this is from watching someone who had performance programming done and after a couple of months all kinds of problems just suddenly came up and they had a heck of a time tracking it down because they were relying on data from the part that was at fault.

 

It's not credible that all those problems emerged at one time.
I'd check the alternator & battery connections, grounds etc..
But I think you should replace the alternator - I imagine it's guaranteed.