Do one window at a time. You will get better and better at it.
You are going to use several HUNDRED screws. Myself, I bought them at eBay as it was cheaper. I replenished my stock last month, paid $6.75 US for 100 screws.
Count the screws on just one window. Then count how many windows you have. It adds up. I would never buy them at a local hardware store or Canadian Tire. Local hardware stores tend to sell screws 4 or 5 in a package. I think Lowes price is something like 4 screws for $1. Thats $25 for 100 screws. Pass. Odds of me finding 300 of them? Zero. No thanks! And realize wherever you buy them, they are all most likely from China. I think some of mine were actually from Taiwan, which was a surprise.
As long as you are not going to paint
the outside, do the windows NOW. Myself, I do everything I can to NOT paint
these trailers. Reviving the old gel coat is cheaper, less work, and to me at least, looks better. Randy has a fleet of Trilliums, he has polished them all! Now on the broken egg Dave had, where the roof collapsed. That trailer will have extensive fiberglass repair. At that point, painting
is the right choice.
The framing is basically held up by the windows, and the wood holds up the windows. They both assist each other. As long as you don't put a lot of weight
on the top bunk, I would just replace in kind, 3/4 plywood with an angle cut. Use the wood you remove as a guide. Use a table saw or a circular saw.
Original wood lasted 40 years (actually, 75% of mine was still good, so it will last longer). I see no reason to go with anything better. And chances are, your trailer was not well maintained. Since you will likely maintain it better, the replacement wood should last even longer, right? I'm an engineer by trade, 40 year life is excellent. Wish my car lasted 40 years with no maintenance. I would call 40 year life a rousing success!
If the wood is good, keep it. I found maybe three or four rotten pieces. The bottom and one side on the front, and one on the back as I recall. I replaced those. The screws will tell you first. If the screws are rusted and the threads rotted out, then you've had a water leak for a long time, and the wood is likely rotten. Probe a little. Truth be told, I had a few screw holes that had a little localized rot, but the wood was solid. On those, I did the hot melt glue and toothpick trick to reinforce the holes. Its a judgment call.
I learned what I know mainly from David Tilston and Randy Bishop. Read their threads thoroughly. Don't try to create new shortcuts, just follow the lead of the masters (Randy and David).