Re: Bugs. Only thought I'd have related to that is maybe including a number of NPCs, possibly unique or limited to specific spinners, who could diagnose/fix your machines. Maybe a quest involved to open up access to them. Possibly a code-breaking and/or Electronic Warfare tie in?
Questions: Would the bug be recurrent or single shot? Would particularly bad rolls turn the bug viral and infect other components? Would having many bugs in the mecha increase possibility or severity of activation? Would the degree of roll failure affect the severity of the bug or would it be a boolean bugged/not bugged thing? Could there be something like that bad mood ability whatsit that could turn a buggy mecha into (at least occasionally) a good thing? Virus guns for inducing bugs into enemy machines?
Re: No-roll. Definitely would reduce urge to scum. On the other paw, it would also negate the chance of a lucky roll and a really impressive piece stuck on a low level mecha. The bug thing might make that better; could still have sensor 10 in my Buruburu, it just might occasionally explode. Note: If explodes, should be large enough blast to engulf other mecha, heeheehee.
Re: Upper rank M.Eng. Maybe higher ranks -- above the 'cut-off' point -- M.Eng could allow for a degree of parts customization? Weight reduction, minor DC increase, armor improvement, etc, etc, etc. Combining it with the bug thing would still be viable.
Random: Perhaps some sort of failure would render parts unrepairable by most/all garages; presumably you'd have done something mechanically horrific that still works, but the garage boys just can't figure out how the blazes you did it. You'd still be able to personally repair it, but the repair roll would be higher or somethin'.