Regarding the UHMW nuts: They should not be tilted. That's what's most important.
I could never get them seated all the way in those cylindrical hollows in the X left end and right end pieces. Those hollows are on the underside of a printed part, so it's not possible to print them precisely, so you would have to carve them down to full depth somehow if you want the nuts to be flush. I don't think it matters.
The UHMW nuts should not be tilted, they should be securely held in place so they don't shift, and the horizontal steel rods need to be parallel with the frame bottom. That's all that really matters about the UHMW nuts.
Regarding the other hardware you mention, and the bags they are found in: I have no idea where any particular item will be found in the kit now. I was an early adopter, and I got a collection of unmarked bags that are notably different than the ones shipping now. And I got an incomplete Bill of Materials that had errors. Other people are adding the details about which bags are which now.
When I got to a point where I needed a particular part, I looked in the bag I thought it should be in, and if it wasn't there, I just searched through the pile of remaining bags until I found the right part. More than once I had to obtain additional parts from Deezmaker; I think they have the BOM straightened out now, so other people will probably not have to do that. I had hundreds of photographs of various generations of Bukobot to refer to, and I could ask questions, and that's how I built mine. I am relying on others to tell me when I've done things wrong. I am still re-photographing parts of the build, to more closely resemble the kits being shipped now, and there are probably still things on my printer that Deezmaker would consider wrong. I have still not powered it up!
I'm not an expert on the Bukobot; I'm just one of the first Kickstarter supporters to start documenting a build. I have been assuming all along that other people would find all the errors and omissions, and complete the documentation. HINT HINT HINT