OKay, let's try this again.
While I do agree that the top surface of that frame rail does look nasty, looks can be deceiving. Once the frame is exposed better and all the crap and crud removed, then a better evaluation of that surface can be done. Since it looks an awful lot like what mine did when I went digging, for me i would be patient and do the archeology to be sure.
As for that sill, I have to say that there is not enough metal left there to act as a attachment point for any kind of patch or repair strip that you might create. However, don't cut it all away just yet. The remains of that seam can be used as a guide or reference for when you install the new inner and outer rocker panels.
Now, before any tool or engine of mass destruction gets applied to the carnage, a very strong suggestion here; TAKE PICTURES! Lots and lots and lots of pictures. And, if at all possible, download them to a printer and make hard copies. Why? Because it is easier to surf hard copy when it comes to pictures, and you have a lot of them to review, than it is to surf a screen. Plus, if you need to compare pictures for details, having the two pictures physically in front of you to compare makes it a lot simpler than trying to rock and roll back and forth on a cell phone screen. And beyond that, what your pictures are, collectively, is the start of your build book, a bible or history text for what you did and how you went about it. Insurance companies love pictures when it comes time to assess value, even Hagerty for the vintage and classic crowd.
Oh, and they also can be posted from time to time to placate the curiousity of the various denizens of this board/fora who are perpetually interested in the mechanical goings on being undertaken by the rest of us, as well as posting what they are up to from time to time.
Once you have given your ride its 15 minutes of cell phone celebrity status, you can then take tools in hand and proceed to open up the lower areas of the A pillar beside the body mount, and the leading lower panel just after the door on the quarter panel. In these locations is where the inner and outer rockers begin and end and it is in these areas that you will also have to investigate to see if there is damage or rust out. I got lucky when I did mine but had to replace the whole outer skin of the A pillar from the seam at the firewall back to the door because it was done. That let me get in behind and inspect the inner surfaces to see if they needed work. In the A pillar this is a high rust zone because it is an area where moisture can accumulate and there is no way for it to dry out.
A lot of work and invective later, once you have cleaned everything up and can see what you have, and after you have had a wobbly pop and digested what you have encountered, it might be decision time. it all depends on the amount and extent of the hidden damage that you just uncovered, what you will want to do next.
Going with the best case scenario here, when you got those panels removed and dug into the recesses, you found some minor rust and crap that could be cleaned out and rust killed fairly easy; no holes, swiss cheezed ribs or bracing, and no orphan stumps leading off the nowhere.
You've been able to either find an inner rocker panel from a donor? ( insert exclamation of surprise and unlikelihood here) or scored some flat body metal and made a panel so you have that cleaned and rust coated and rust primered or shot with a layer of weld through primer, the plug weld holes for the install punched or drilled, and ready to install.
When you go to do the install, ONLY tack the panel at the ends, in the A Pillar cavity, and to the drop panel in the quarter panel cavity. DO NOT attach it to the existing remains of the sill. Why? The sill is your reference point but you, from what all the threads you have posted indicate, plan to do the whole floor pan, so that means a new sill as well. Therefore there is no point to picking up the existing sill with tacks. You might be able to use vice grips to create and maintain a mechanical connection while the rocker panels are going in so you can maintain your panel alignment and seam height but what you are likely to find, if you have not noticed it already, is that the flange on the floor pan outer sill actually points down! That is why there is that huge strip of body seam sealer present and that is also why that seam tends to rot and rust, moisture and crap from innumerable entries and exits gets caught in there and provides an ideal venue for the tin worms and cancer to rear their ugly heads. This method of construction was the factory's idea and did not take reality into consideration from time to time.
A thought here, it is possible to finesse the system. Just as an idea, that down facing flange is part of the sill strip that is not a part of the floor pan section. That gives you the option, when you measure for, cut, and bend that strip, of either making the bend so as to have the flange point down, or you can elect to make life a little simpler and make the bend so that the flange will point up! No, that is not the factory OEM way and the purists will be outraged but, having the flange pointing up eliminates that seam site so no place for rust to start. it also gives you a third layer of metal for the rocker seam, it makes it easier to attach the inner rocker to the door sill if you chose not to go with a rotisserie, you can make the horizontal surface wider than necessary to give the pan something to sit on and make it easier to go with a lap joint and, instead of relying on just plug welds for your connections, you can actually run a top bead along the edge of the three panels to lcose them up completely. The third layer does not appreciably thicken things as a whole and that plastic wire sleeve that fits over the sill flange still will snap into place and position without too much encouragement.
So, summarily, get the inner and outer rocker panels in and nailed down securely first. Although it might not be thought of as such, the rocker panel assembly is a structural member in that it provides a strong physical connection and bridge between the lower A Pillar and the rear infrastructure of the cabin. As such it establishes and maintains the lower shape of the door opening so that the door fits into place correctly. This another reason that you want to keep that sill in place temporarily; it gives you the exact height for those rocker panels beyond which the door will not close but wreck on them and jam up.
And yes, you would be right in thinking that having all those braces that I mentioned up above in place would also serve to keep the door opening from moving but if you do the rockers first, before you disturb the cabin or remove it from its rubber mounting biscuits, then you can minimize the amount of sweat equity that might become necessary to re-establish the proper shape for the door opening. This is a T-top tht is under the knife here and that means there is very little roof structure present to help the cabin to keep its shape. So don't be stingy with those braces.
Nick