If they said it wouldn't seal because the flange surface isn't flat, then just fix that. If it was because of the mangled threads, use a longer stud with a nut on top like you planned but you don't need 12.9, 8.8 will be plenty because that's already better than what GM used. Get one of the Remflex turbo gaskets for insurance, and don't over tighten the bolts. I know at least a couple of the vendors here sell them, or you can order direct.
[PS Yes, I'm bored, so I did some quick and dirty calcs and 8.8 10-1.25 will give at least 6000 lbs of clamping force at a 50% yield margin, and a rough estimate says it will take about 5-8,000 lbs of force to break off the corner of the flange, so I can't see where more than that will gain you anything.]