Since "permanent" code existed when you bought, previous owner had been clearing the code repeatedly.
If hole is upstream of the catalyst or O2 sensors, it could interfer with sensor readings and/or cat performance and cause problems. I doubt there's an impact with downstream leaks.
Bad pre-cat sensors can certainly cause cat codes, but I don't see from report that they are problems. What am I missing? You don't have sensors 3 or 4, so those "not availables" can be ignored. DME is clearly in closed loop mode with fuel trims being reported and fluctuating. No harm in replacing O2 sensors though. Report says post cat sensor output is .9999v with a max allowed of 0.9218v. This is likely the cause of the codes. If you want to experiment I would replace (1) pre-cat and (1) post cat sensor on the same bank. Diagnosis with a BMW specific tool like ISTA might give more clues, but in all likelihood your cats are bad. Prolonged running with misfires could have caused the damage.
If engine is down on power, trans will shift hard. Fluid change may or may not help with shifting. DO NOT use ATF in the transfer case. It likely needs friction modifiers like that used in LSD's, since it's clutch pack is expected to slip.
Factory engine beauty cover has soundproofing. I wouldn't try to improve on it.