I have the same setup. I was initially concerned about the same thing with the fit of the upper doors and the rear bulkhead. After a few trips, it's not a concern for me any more. The fabric upper doors were the last thing I needed to enclose the cab, and I am impressed with how comfortable the cab is in the cold. I put a coat on and it isn't long and I take it off, and am cursing around in a short sleeve shirt. The Honda heat problem keeps the winter cab warm. And the upper doors come off in two minutes.
The other side of the coin, I find Honda instructions suck. Often, the only way I can understand what the heck the instructions are trying to explain is to fool with the part long enough to get it properly fitted, only then do the instructions make sense. It is this way on every Honda accessory I have installed! (It might just be me, I am getting old).
The other thing, Honda accessories are not compatible with Honda accessories. I had Honda outside mirrors that won't work with the upper doors. I have a inside rear view mirror, but I need the two out side mirrors to back up on small narrow trails.
I am open to suggestions on outside mirrors that work with the Honda upper doors if anyone has found them.
By the way, after installing foam strips strips to fill the big gaps on the lower doors, the cab is remarkably dust free now!