Can't really provide an answer regarding your PC alignment problems, but I did have a chance to corner an FMF guy recently about all the complaints I see on this forum about problems with their pipe's fit and alignment.
His response was that they use jigs/fixtures to check alignment quality, and there are times when the check fixture is "bumped" or "dropped", and the right people aren't notified / aware of it until after a bunch have been shipped out.
I know, it's a lame excuse for quality control, and I can't imagine that this problem would be commonplace in the aftermarket pipe business. Hopefully PC and FMF monitor these forums, and start putting better quality controls in place.