Some are a real pain in the $$ to line up. I have had 3 TR's and 2 of them were OK, but my 87 GN was a bear.
If they line up OK, you can do this job with the car on its wheels. But if you have misaligned lines like yours, you want to lift your car up so you can get underneath and really eyeball the lines. You've got to be able to see just how the nut is going cock-eyed so you can apply counter force.
Like MSDGN said, do not tighten up the clamp. If you can tell which side is most out of whack, get that side just barely started first, then get the other started, then tighten each side, then put the surrounding clamp on. Good luck.