I want to redo a section of my mod by moving a bunch of rooms from one cell to a new cell. Is there anyway to put the whole large copied rooms in a specific point, the 0,0,0 center point of a new cell?

I can make a suggestion to try in the CK. Go into your new cell and place an xmarker at 0,0,0. Then go to the room you want to copy and place an xmarker at the spot you want to be at 0,0,0 in the new cell. Select everything you want to copy, then hold ctl and maKe sure you select that new xmarker last and then copy everything. Then go to your new cell, select that xmarker at 0,0,0 and right click and choose paste. I think it will align the last item you selected in the old cell (that new xmarker) with the xmarker you placed and selected at 0,0,0 in the new cell, and keep the spatial relationships intact. You also might want to turn off the snap-to angles to keep them from popping to adjusted angles
Good luck.

One other thing. There is also a function to cut and paste markers that retains all of the links but I don't recall the key combination. It shouldn't be too hard to find though. It would keep you from needing to reconnect doors and such but permanently removes them from the original cell.
Sorry, should of edited that. Don't know what I was thinking.