Question...What part of the roof is this????
 

Looking from under the door I see this rust, I don't see it from inside. is this part of the drip rail or the roof frame

Attachment 3546

Attachment 3547

Looks like it a little of both going on there,
Weatherstripping up is drip rail. Part going under the stainless where the rest is. That was part of a interior roof brace on mine.
Once you get the weatherstripping and stainless off to clean it. It is more obvious where the line of the 2 parts are.

How is the weather strip rail held in, is it spot welded or screws. Can I patch it if it is not to bad or do I have to replace the roof and braces too?

Once the rubber is out it is held by screws.
Clean it up with a wire wheel and metal treatment. Cider vinegar is a real good rust inhibitor. Or rust coverter which is alot more expensive and does the same thing. Stops the rust process in the pores. Epoxy Primer stops it from restarting by sealing it. If you got pinholes just paint fiberglass resin on it before priming.
As long as the drip rail is still decent it won't leak. And get in there starting it over. You can patch the roof rail parts if needed. It all covered up into the interior anyway.
It don't look to bad now if you stop it. Just scary looking. Once it is cleaned it looks like there is plenty of metal left.

Rust conveter only scratch the top surface. That piece like said is removed by the screws holding it on. Be careful with it, I don't think they repo it. Only true way to deal with rust is sand blast down to clean metal.

Thanks for the info.... gonna start on it this weekend...I'll be sure to post pics on the progress