Trial fitting the mounts. This involved removing all of the other engine mounts and twisting the engine to one side in the frame to allow the rear mounts and bolts to be installed, before wiggling the engine back into place. It also showed up a few clearance issues between the mounts and the swingarm (see pic below). To avoid having to move the engine again, I used a die grinder to remove material with the mounts in situ. Eventually, with a little bit of grinding, the swingarm bolt went through, the spacer was seated nicely in the rear mounts and all of the rest of the engine mounts tightened up.
With the spacer now fitting nicely in place, all that remains is for the mounts and spacer to be welded together. Once that's done, engine mounting should be taken care of and I can move on to solving the next problem...