I did not think to check them with a straightedge. Good idea, I'll do that tomorrow. I drove it to work today, so it'll have a few heat/cool cycles before I get it back on stands tomorrow for oil change, etc. I'll retorque those bolts.
If the flanges are indeed warped, will doubling up gaskets help or should I just look into a new exhaust anyway? Everything that I can see from the downpipe back is also pretty nasty. I don't know if this car was ever maintained by the previous owner beyond oil changes and fuel fillups. I have a receipt from when they took it to a dealership to get the wipers replaced in like 2004.