Definitely looks mis-alligned.
On the stock pipes, the flange that mates the front to the turbo, triangle with 3 bolts, is a PITA to get correct, due to the O2 sensor location on both sides (wideband O2). It is almost directly in front of one of the bolts.
On aftermarket downpipes this is corrected, and they are much easier to bolt up to the turbo.
When my dad and I installed my SW downpipes, it was a real pain getting the stock ones off due to the O2 sensor, but we managed. We bolted in the front of the downpipes slightly, then the rear, then tightened the front, and finally tightened the rear. Much easier with a second person to apply pressure. My SW pipes also are both one piece, so that makes install much easier.
Putting the car on ramps should afford you what you need. I would loosen the back flange, and middle, get the middle squared away, and then re-tighten the back. Double check connection to the turbo as well, as a leak there would be detrimental to performance.
