Josh the shop manuals I have don't list the height of the collar, the only way for me to determine it would be for me lift my car and crawl underneath and measure one but that's not possible today. I would guess they are about 12mm; if you were to use one nut and a washer between the mount and frame that would be an improvement over the setup you have now until you can source them.
Regarding your alignment problem along the longitudinal axis of the car, can you take photos of your De Dion tube where it mounts to the car, front and rear, including the Watts linkages, your tranmission mounts, and post them?
Regarding your noise. Have you carefully looked for signs of metal-to-metal contact all along the drive line? I recommend you crawl under the car and inspect all eight flywheel mounting bolts. If one has vibrated loose and backed out its head can contact the front flex coupling mounting studs that are pressed through the flywheel as the prop rotates. This can shear the head off the bolt, then you're in for some real time and money. You'll need a flashlight and a 17mm wrench to rotate the prop shaft.
Good luck!