Once you get your doors where you want them, I recommend that you do not remove the panels prior to spot welding. You don't want anything to move even slightly.
I drill the panels in place. I use a regular drill bit big enough (3/16" maybe) to allow me to reach the inner panel through the hole to get that underlying panel red hot to start the weld and them move it toward the outer panel for a sound plug weld. I use a TIG welder, but the same method works for MIG.
As far as where your screws are located, you can remove one screw at a time and drill your 3/16" hole in the outer panel and weld it up the same as above. The weld will fill that tiny screw hole in the underlying panel as though it wasn't even there.
Be careful not to drill through the underlying panel when drilling, as the drill bit likes to grab that tiny screw hole and keep going.
