Fitting the cover must be interesting. Another observation, I assume you have 2 piece barrel/head bolts. There should be more thread sticking through the nuts unless you are using full width nuts. My bolts just sit proud of my lock nuts. Also, is there a washer missing from the RHS head bolt? Your bike appears to be about 28 after mine so I guess they were made in the same week.
The cap overhangs the mounting face a bit, yes. I expect sealing will be a bit chancy, but I have the Videan cap rings, so I hope that helps.
I noticed the inner bolts seem a bit far into the crankcases as I put on the head brackets, but didn't want to disturb them. That is where they were after the rebuilder finished up. He had to remove the inserts deep in the crankcases to clean out some bead blasting debris that I noticed as I (re)started the project two years ago. (It wasn't me..) At that point I decided to get some expert help, and I am glad I did.
The rear bolts are all flush with the lock nuts. I have the original 2 piece bolt head nut parts, and these SS replacements have the same dimensions. I can't see anything it affects since the spigot nuts have full thread engagement, and I am not using the oil galleries to the cylinders. I will have to find a different way to mount a hydraulic steering damper though, since there is no room for a bottom end bracket under the lock nuts. There is a washer there under all the nuts, matched for thickness, just not a good picture. The spring and seat is also centered in the pocket, but the angle of the camera makes it seem offset.
The engine left for Canada in the last days of October 1948. I think it was completed around the same day I was born in 1948, so it is my twin, in that sense. My UFM was shipped to the same small Canadian dealer in July of 1948 and somehow ended up with its brother engine . It is things like this machined pocket on this is 65 year old machine that amazes me that they are still running at all, let alone happily and frequently and with no significant disadvantages when even slightly modified for modern traffic. When I left the Navy and came to Maine, I worked at a small company that made winches and net reels for the fishing industry. I learned to be a machinist on old equipment that was pre-war and worn out even in 1978. I found out the meaning of fettling and selective fitting during those years. In these days I deal with multi axis CNC, CAD, CAM and 3D printing, and I really am in awe that the people at Stevenage could take a sheet of paper and design and produce something like the Series B so quickly and really successfully after WW II. I guess I can understand a few machining glitches on the machine.
Ron