No transmission is bullet-proof - if you abuse it, you're gonna break it. The 6MT is pretty stout - some people on this site are FI'ed and running stock 6MTs with no problems. You should be able to find more than one thread on this site about beefing up the 6MT (IIRC, there's not a lot you can do) and how to use the 6MT properly. Personally, I'd get a reputable shop to rebuild the trans; might be able to find some beefier synchros to put in there.
The speed/rev nannies can be adjusted when you get your tune.
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