Long egr pipe broken bolt ?

[mustardbucket107]

Working on my pickup last night and taking off the long egr pipe, one of the bolts twisted off with approx 1/8" stud sticking up. We are going to weld a nut on it today to get it out. My two questions are what is the best bolts to put back in there, gr8 Allen head? And while tacking that nut on should batteries/pcm/tcm/etc be unplugged.
Thanks

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