I do it in 3 steps:
Step 1: I lay down the new pan on the old pan and use self tapping screws in a few places to screw the 2 together...I then trace the outline along the trans tunnel side and where the corner comes around the back radius(in other words, I am tracing the areas that get butt welded)
Step 2: I take the pan back out, cut about an inch lower than the line I traced...I also drill out all the spot welds along the inner rocker, the frame rail, and the rear ledge...removing ALL the old metal except the inch I have left from my tracing line
you can see the original trace line in this picture...easy enough to see on a light color panel...just used a carpenter's pencil...on a black panel a silver sharpie or a soapstone is better...or even a score line using a nail.
Step 3: I then lay the new pan back in and retrace my original line...this line usually moves about 1/4" lower than it was before. I take the pan out and cut the newly traced line...this is what I end up with:
As you can see, the fit is so tight you can actually TIG weld it without using a filler rod or filler wire(not that I am using a TIG welder in these pictures...but that is only because I am not much good contorting myself around in a car while using a foot pedal...but it could be done)
P.S. I only butt weld the areas where its patched into an existing panel(IE, I butt weld the trans tunnel side because I am "patching" a full floor panel...I spot/plug weld everywhere the factory did)
P.S.S. And yes, I end up with a good dozen extra holes to fill...some like those near the seam line I drill to be able to get a hammer claw on a self tapping screw to be able to pull on it for panel alignment so its flush. Some of the self tapping screws like the ones at the frame rail are to make sure I pull the rail lip tight to the pan for plug welding