I used 3/8" closed cell neoprene foam for my padding. r.d. enterprises sells it. Since you're on the west coast, I would call Ken at Dave Bean because they probably sell something similar. The section of the padding that goes on the 'T' is probably about 1/2" thick or maybe a bit more. There is also a triangular shaped piece of padding that goes where the frame Ys out. That has a rubber cover on top of compressed jute It's probably about 3/4" or more thick IIRC. Ken or Ray could probably advise you on dimensions. I still had that piece so I used it. If you don't have yours, you could make it from several layers of the neoprene foam. The foam provided a very snug fit for the body to the frame. I would not use jute.
You should not have to use the neoprene washers you're talking about and in any case, I would advise against them because it would allow for compliance between the body and the frame. You want them to work together as a single unit.
I didn't shim my body and I didn't mount it on the original frame (so there was a potential issue with tolerances. i.e. it's unlikely the original frame and my new frame had the exact dimensions and thus the fit would likely be a little bit different). As I explained earlier, it didn't even occur to me since I didn't remember any shims between the body and frame when I took it apart. I could imagine some minor space between the body and frame and I could also imagine that it might be caused by the snugness of the pad and a little flex in the body - again, I didn't experience this or I wasn't aware of it - so if the gap between the frame and body was the thickness of a washer, I think I would just tighten it up without the washer. If there is a significant gap, I might shim it then but I might try tightening the bolt listening for signs of distress from the body first. It could be that the frame is hung up a little rubbing on the padding and twisting enough to look like there's a problem.
Full disclosure - I have only mated one body to a frame so my view may be a bit myopic.