Megan does suck so I'm not questioning the possibility that the flange is angled completely wrong. But I'm curious to what catalytic converter and catback you are running. You do realize that the 94-99 GSR header and cat is shorter while the catback is longer right? If you mix and match parts from an LS, ITR, B20 or 00-01 GSR they wont fit right.
The 94-99 header is about 2" shorter. The cat is about 2.5" shorter while the B-pipe is 4.5" longer to make up the difference. All of the coupe axle backs are the same