Can't help much with the door seal lip repair, other than to say that doubling up the metal, either on the body or the lip, doesn't seem like it would cause an issue as long as your additional metal isn't too thick. I'd take a good look at it before doing it, but I don't think you need to butt weld your fix in. Ideally you could get to the backside.
Regarding the stiffeners, there are quite a few how-tos out there that will give you a much better idea than I can in text. I cleaned off ALL of the rubber undercoating with a wire wheel. Marked both the body and the stiffeners where I as going to weld (skip along perimeter) and removed all paint from body at those locations. The rest I just scuffed up a bit. Weld-thru zinc primer the whole area. Full paint prep on backside of stiffeners and weld-thru zinc primer. Seam sealed the perimeter except for a few gaps along the bottom, then paint and undercoating.
Angle the weld wire more towards the stiffener than the body (so not the usual 45°), start welding into the stiffener and then draw it over onto the body, spending more time on the stiffener than on the body. You'll get the hang of it soon enough.
Then clean-out the inside of the frame channels as best you can and paint the backside of where you've welded. i used Eastwood products with the tubes.
Rear wrap-around stiffeners are a bit of a PITA to install because you need to push at an angle to form them into place, with the top corner being the worse since you need an "extension" on your jack. Just be prepared for wanting to push forward on your XJ when putting it up on stands. Make sure you have it where you want it before pulling the trigger...
I'll forewarn you, if you're like me, it starts out as just a stiffener install and then you look a little bit to the inside and see that oil covered mess and the "while I'm here" syndrome kicks in and before you know it the motor is out. To do full front to rear stiffeners, you're going to want to have both axles out, or darn close to it. Before you know it, you end up with 2 XJs because you couldn't get the 1st one back together before winter...
Depending on a whole lot of factors, I personally would not add stiffeners just for this repair. The risks of the stiffeners causing more issues with rusting out of the frame channel is higher than the benefit with regards to fixing the rusted out hole. I personally would get a set of shackle relocators that bolt to the underside of the frame channel (HD Offroad Engineering comes to mind) before I'd add stiffeners if the sole purpose was to fix the issue at hand. That being said, I have stiffeners on both of mine.