TESFaith is fantastic, but as many other tools still a little beta so we have to spend a little effort.
Moving TR: too big, and hey, should not we be doing all these efforts to be compatible with it?
In my experience, assigning all cells you want to move to a region before moving often helps if standard method seems to skip cells; problem is, if you want to keep the region, you'll have to blank (make Wilderness) the cell names else the in-game map will show a lot of cells with the small "explored" square.
TESFaith scripting warnings are a little generic (no real need to check interior relocations or for GetPos/SetPos Z commands), but generally it is always better to check the signalled scripts.
On occasion, I had some strange problems with some teleporting doors missing after the move (I.E. Wizards Island Cathedral exterior ladders), it may be related with the sheer mod size and/or the fact that teleporting doos were exterior to exterior, I don't know, so better World Testing/Non teleporting doors before/after in TESCS
Hope this is understable, I think I asked too much to my poor english syntax, LOL