I see. This is pretty much the approach to what I did for the rafters, cut back to good material and sistered in two pieces of plywood with filler between. Mine had an advanced stage of "water cancer" and I was able to recover the patient fully. I must have used 20 tubes of construction adhesive in the process, every piece that was replaced got a liberal dose of adhesive when joining.
One of the parts of the process that held up time was removing the thousands of staples and screws holding the siding and roof to the top plates and framing. In retrospect, I could have made better use of a sawzall and grinder rather than trying to pull them. Since I did my project, I now have one of those small reciprocating flush saws. That would have been an excellent tool for the job.
Painting aluminum: Any bright or mill faced aluminum needs a primer for good bond. It is all about the fast oxidation of the surface of the aluminum. Commercial fabricators of aluminum parts will maybe anodize, prepaint. Either that, or apply an etching primer that reacts favorably with the oxide on the aluminum. Both of these steps are beyond the kin of the usual handyman. The Sherwin-Williams Industrial DTM primer is very good, better results than the two-part process of etching and primer, IMO. I would assume it has a blend of etchants in the formulation. The good news about the SW DTM primer is that you can source it just about anywhere in the US at your local SW dealer. Some don't carry it as a stock item but delivery is usually in a day. You can brush, spray, or roll it on.
Painting the inside surface of the aluminum sheet isn't going to net you much in the way of durability or function (unless you camp every year at sea-side). If the price of the painted sheet is similar to the unfinished, I'd choose painted every time.
Here is a picture of my front rock cover made from vinyl coated aluminum sheet goods. The cover is the same now, (3 yrs.) as the day I made it:
Picture of roof after applying two coats of elastomeric roof paint: