One of the bolt holes on the shift linkage lever(the part that attaches the cable to the trans and is what actually physically changes the gears on it) is stripped out and I'm planning to put in a B&M shifter soon, would simply retapping the threads to a larger size be sufficient?

sure, that or replace the arm. or you mean a trans pan bolt? again, drill and tap, or a heli coil i suppose.

some of the bolts are drilled all the way though the case, others are not. be careful no to drill into the trans and make a leak

So a longer bolt might even fix it? But whatever the fix I need it to be pretty strong given the application. And the bolt holds the shift lever to the trans, but it also goes through the pan.

I'd heli-coil it; lucky for me I have M8x1.25 heli-coils in the garage.
If the bolt hole goes through the case to where a nut will fit it, that would work but be annoying.

never said anything about a longer bolt, but probably not. I would try a heli coil first

Yup, Heli-Coil is th eway to go.