Pat,
I think I may have a newer version of the service manual then you do. Mine includes the Thruxton as well as the rest of the Bonneville line. According to my manual it's fairly clear;
(this is directly from the manual)
4.) On America & Speedmaster, the alternator rotor has two lines, marked 'L' & 'R'. Align the line marked 'L' on the alternator rotor with the crankcase joint at the front of the rotor to bring the engine to its timing position.
Hope this helps.
If you want the associated pictures just let me know and I'll either scan them or copy and fax them.
Keith
