I have never built a complete body but in making portions of the body if you have something to copy, then you simply copy it. When you are talking about functional parts like you are, this is easy, you copy an existing example. The windows you could simply copy a 32 Ford or Model A, use the same regulator and all. But you could also make it from scratch as far as simple universal channel found in the glass supply places, there are all kinds of thicknesses and and come in something like 5 foot lengths. Often they have a very stiff metal inside it so you don't even need a channel around it. At least not the whole way around. In my 48 Chevy pickup it has small metal channels down the front and rear of the door below the belt line, just simple 1/2" U shaped channel. Above that, there is nothing, the felt lined channel is screwed in with small screws thru the bottom of the channel, that's all there is above the belt line.
The regulator, just about any early car all work the same with a scissor action that can be duplicated in your home built door with just about any regulator. I put power windows in my truck back 35 years ago when there were no aftermarket stuff like this. I simply got a power window regulator out of a 63 Buick. I measured the distance on the stock regulator from the first pivot at the motor to the scissor action center pin. I cut the regulator off in half at a point in the middle, I cut the power regulator so that when I welded the original piece to it so the pivot points matched the original, then installed it with the pivot point at the same location in the door, worked perfectly.
But using the rubbers and stuff from another car and making those mounting points the same as the original car allows you to use all the engineering from the original car in your body that you designed.