Attaboy, hard at it!
For that unprotected seam and for around windows and doors I used protect-a-wrap, a 6" wide self-sticking window wrap. It is waterproof and offers some protection to the frame in those areas. I also used small cut pieces under the marker lights, just made a small hole to lead the wires.
You should end up with a nice paint job if you're stripping all the siding. I just had a couple areas of bare metal but I primed all of the siding. I used Sherwin-Williams DTM Industrial Primer. It is a real good primer for aluminum. I chose to use conventional siding paint as I have a lot of experience with it and it is very durable. Of course, if you want something that ends up like a show car, a guy can use auto body paint but I couldn't justify the cost. I applied all of the body paint with a Graco airless sprayer and a fairly small tip. I'm real happy with the paint and get a lot of compliments.
Keep the pictures and commentary coming, we all like to see how it's done.