I just replaced the drivers side floor pan on my YJ this fall. There reallys wasn't much left of it, and the Q-tec panel didn't even fill in the hole, although I could have made one I opted to buy the Q-tec one. Once it came and it wasn't big enough I just added a couple filler pieces to make it fit my very large hole.
The panel can be fabricated, but with all the angles and such I decided it was worth the $50 to not have to mess with making one...
I repaired mine with the tub still on the frame without issue. I also repaired some tub rot and a couple small holes on the passenger floor. I then put in bedliner (Herculiner) and no carpet.
As for tips N tricks- I used a few self tapping sheet metal screws to hold the panel in place then did very short (3/4") stich welds, one on each of the four sides to keep the panel from warping due to the heat. I then kept filling in stiches (spaced apart) until all the stitches met. I then removed the screws and filled in the holes with some more weld. I did the same for the underside in the spots I could reach. :-)