I'm about to tackle mine, sills and all, and I plan to X the door opening only. The way I see it is the part most likely to get knocked out of alignment is the hinge pillar so I'm going to concentrate on keeping that in place. The firewall should hold side to side dimensional stability while cutting out the parts that maintain the distance from the bottoms of the door openings indicates that it's wise to brace that area.
When I get the floor pan and sill tacked in I'm going to cut the bracing out and final fit the door, then skip weld the patches... and I'm only going to do one side at a time. If the doors fit and latch shut everything else should be simple.
I also plan to put the brake and clutch pedals and the steering column in to check their alignment with the holes in the floorpan.
Start with the Passenger side... there's less stuff to line up on that side so it's a good place to get a feel for what you're going to face.
Rule of thumb: Always start on the Passenger side because you don't see that side as much as the driver side so if you screw something up you don't have to look at it every time you get in it... don't laugh, it's a well known trick in the bump shop biz.
Go slow, tack everything, make one last check then weld about 2-inch beads skipping around so as not to concentrate the heat in one area.
