I own an '87 non turbo 944 and am in HPDE4. The original engine blew at Mid-Ohio in April 2014. I had a good low mileage engine rebuilt and installed in June 2014. Since the replacement engine was installed my exhaust system has begun breaking at the weakest point. The first break was post cat. Welded that break then 2 sessions later pre cat break. Welded that then next event cracked header pipe just below flange. I think I have an alignment issue with the drive train. Looking for any feedback before I take action.

Incorrect balance shafts alignment?

I would think either it's just time for those things to break and you're just having bad luck with the timing of them or like Joe said the balance shafts may be out of time vibrating everything too much. It could also be a bad motor mount