Been there done that a few hundred times!
in the pics you have it clamped in the correct position etc.
First off, keep in mind that your a pillar / door post is not supported. You might have to jack it up as they tend to drop when the rust mongers are cut away. I have had them drop as much as a 1/2 inch.
Second finish cutting off the outer rocker. Leave the inner rocker / floor part under it.
Screw it all together including the outer rocker, then mount the door, use the roof and cab corner as a guide, make sure the rocker line is good gap wise and flush with the door the whole length of it. Make sure the door doesn't rub on the rocker when its closed. DO NOT weld anything until you make all the adjust ments. I use hex head 5/16 self drilling screws to hold it all together. If things don't fit good you can unscrew and adjust.
Something else I do is tack weld the cab mount bolt nut in. The sheet metal cage that holds it from spinning some times gives it up. I also replace the flat part which covers the mount nut and ties the rocker / floor support to the cab mount with a piece of thick sheet metal. This give you something to plug weld the floor down to.
Here are some floor panel pics.
Looking up from the bottom. Notice the plug welds all along the floor suports etc. I get it fit good then trace around the suports for a guide to drilling the plug weld holes.
The top side of the floor.'
Screwed in place.
The end toward the cab in the pic is the front. What is facing the camera is the top of the outer rocker. You see I have plug weld holes in it to weld it down to the inner rocker.
You see the plug weld holes on the bottom lip to weld to the inner rocker?
in that pic I have it screwed into place.
Same goes for the cab corner, in the pic notice the plug weld holes.
Dont drill down to far on the front edge of the corner, its a pain the grind the weld down close to the rocker.
Checking the door fit here.
All welded up.
Drivers side welded up, and getting the once over from the boss!
Primed and seam sealed.