Yes, you can in theory over-torque an exhaust flange, especially with an air wrench (which what I assume you mean by torque gun). The primary concern would be that you overtorqued one side before the other side was sufficiently torqued, which might warp or bend the flange. Stillen's instructions should have the correct torque values, I don't recall them offhand. In general this stuff should be done by hand (as should all tightening, and then use a torque wrench to get the correct value if necessary. You really only use an air wrench for loosening things in most car applications).
All of that said, unless you went really crazy with the air wrench, you're probably ok. If it's not leaking, just leave the bolts as they are. Loosening and retightening could make things worse if you've already overtorqued (like cause gasket failure). You did use anti-seize compound on the bolt threads right?
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