The up pipe brackets are pretty robust but that's what I was going to suggest but in all honesty you shouldn't have had to touch them to just pull the trans.
You can see the one very large bracket in this photo...
There might be SOME movement in the bolt holes but I don't remember there being all that much and since you had this installed once that seems very odd to be giving you issues now.
I had issues with a CNT pipe fitting my car and I had to completely loosen all of those brackets as well as the up to turbo bolts to move my turbo ever so slightly to the drivers side because the pipe was hitting my cross member... Once that was fixed the one I had would no way in hell sit on the tail shaft bracket because the mount was just completely in the wrong spot so I just returned it and now I have an Invidia that's going in soon.
SO worse case is loosen up all of those brackets and bolts and just bolt the down pipe to the turbo.. position the dp where you want it, secured to the trans bracket and then tighten the mounts and turbo back up.