Yuck. You want to get that metal as shiny clean as possible to remove all the rust. A wire wheel can get into the channel, but I find that sometimes don't do much once all the wires bend in the direction of the rotation and clean little. I find that one of the
Shaft Mounted Polycarbide Abrasive Wheel type wheels work better. You can get them at Harbor Freight and I think Lowe's and Home Depot have similar.
3 in. Shaft Mounted Polycarbide Abrasive Wheel
Once you get the channel as clean as possible, I would spray the channel with spray bomb Rust Reformer. Let it dry good. Then come back with the abrasive wheel and sand the channel again which will leave the rust reformer in the pits and seal them. WTF your say? You are going to use fiberglass cloth to go over and cover the rotted channel so you want a clean metal surface for the fiberglass to stick to. But first......
If you have some thin aluminum, or sheet steel, cut it to the lip height and shape it to the areas you need to fix The channel will have a roll or radius at its bottom, but I would only cut the strip wide enough to follow the straight side and not the radius unless you have some way of roll forming the piece which can be a little tricky or roll form the edge with a hammer after the JB dries.. I might do the entire channel by sanding the outside of the channel to bare metal and overlaying all new thin aluminum or metal sheet and using the JB Weld to bond the 2 pieces together - you can do this in sections if that makes it easier. Rough up the aluminum or stell sheet to give the JB something to bite into, you don't want a smooth surface. Then put some clamps to hold the 2 pieces together and let them dry. You may have to do a section at a time. Don't worry about any JB that squeezes out - leave it and you can sand it off later as it sands easy.
Once you have done your overlay, now go back and apply the woven fiberglass matt to the inside of the channel. You can buy the fiberglass resin and activator at most auto stores or Home Depot/Lowe's as well as the matt. Cut the matt with scissors as needed to fit the channel sides and bottom - basically reinforcing the entire channel. Work with smaller pieces as it is easier to do. You want to make sure the matt is wetted by the fiberglass resin and no dry spots or air under the matt. Rubber gloves can help. Use a small putty knife or the wife's spatula to work the matt into the side corners of the channel or any place you see the matt not laying flat. Better to have too much resin than not enough and the matt dry. It will set up kinda quick depending on how much activator you mix in. You will figure this out as you go.
When done, you should now have an overlayed outer channel and fiberglass matted inner channel. When all cured, you can go back and apply the JB Weld along the base of the new metal where the radius would be - you can use it like bondo and let it dry but make sure you sand along that area to scuff it up. Then come back and do any sanding or shaping you might want to do with a sanding block. Then you should be ready for primer.
If you are real fussy, you can smooth out the inner channel, but I would use the Short Hair fiberglass bondo for this. Apply it inside the channel to fill in any dips or uneven areas, then sand down smooth. It will be tedious work and not sure worth it if the rubber seal is going to cover it, but your choice. You can also use the fiberglass bondo instead of JB on the outer lower radius of the new metal strip, but I think the JB will work.
That is just one way I might do the job. I could change my mind once I actually started that job as once you get into it, what I thought would work isn't working as planned. So this is just a backyard suggestion.