Sounds like you have a lot of skill work with materials. I have a P36 and try to maintain the original look as much as possible except when a practical change trumps an aesthetic one.
There was quite an extensive thread on these original windows in the distant past. You could probably find it or someone in the group will do so for you. I think the problem with the windows is overrated along with solutions that are over thought, if you get my meaning.
As I recall, the problem had little to do with the basic design, but a lot to do with configuration of the inner and outer skins of the cabin at the location of the windows. Think for example of trying to seal something that has is wavy instead of flat. That is the situation. The skins are not parallel. With the windows removed use a caliper and you will see that the width of the border of the window opening varies considerably.
So you might seal and clamp the inner and outer frames tight at one point only to have it loose at another. The solution, I believe proposed by Dan Pfieffer and endorsed by others is to fill the gap between the skins so that you have an inside-the-cabin surface that is approximately the same distance all around from the outer surface of the cabin. Once that is accomplished, and it's probably not a casual easy job, the window should fit well and be tight. A little gasketing or sealant should make the windows water tight for a long time.
That would be my approach and I have to do it because I didn't have that good advice when I rebedded mine 15 years ago.
The other thing to consider that you may already be aware of is the glass or acrylic that is the correct thickness to go into the window channel is not available. At least I could not find it. This is a problem if your glass is cracked or cloudy. I don't recall the solution, but I am sure someone has one. If the window is to be acrylic, I guess the edge could be carefully ground down the slight amount needed for a good fit.
I like the original look which is smooth and unobtrusive.
Bob Franklin
P36 "ARION"