I have just read Wheels of the RAF by Bruce Robertson which does cover markings, albeit not in fantastic detail, regarding motorcycles.
" RAF vehicles were identified by a service-registered number prefixed RAF. The RAF roundel was adopted as a Service marking in April 1941, to be positioned on the offside of the front of RAF vehicles, where possible on the wing. Roundels were hand-painted using stencils until 1944, when a roundel transfer was introduced. Also in April 1941, a Command and Unit identification letter and number were introduced. In general, the letter was indicative of the command, and the number was the group number or a code number for the unit. This was marked on the front of vehicles, on the opposite side to the roundel, in 5" high white characters. "
Photographs in the book seem to contradict the placing of roundels/unit markings, showing them either swapped around or both on the offside!
The RAF standard MT roundel sizing was Blue 9", White 5.4" and Red 1.8"
" In 1922 instructions were issued to mark RAF on the tank, which some units had done since 1918"
See also here http://hmvf.co.uk/topic/20156-ww2-raf-bikes/