I did check the interior assembly manual and there is no mention of bows at all.
Assuming that Ford didn't make too many "changes" between 1964 and 1966, the information you seek is in the 65 and 66 Interior Assembly Manuals. The first bow in the 65 manual is a 65 Mustang part number, the other 3 are 64 Mustang parts. (All the bows in the 66 manual are 65 Mustang parts). The color code for 65 and 66 are the same:
1st (Front) - blank
2nd - red
3rd - white
4th - blue
The ones color coded are noted "one end". Your choice of right or left.
Secondly, two of the rods had what I will call an adapter on one end, so I am curious what the purpose of these are for. Lastly, how many of the retainers for the bows should I have?
The revisions (10/21/64) in the 65 manual state item was 4 removed. It's description is "Extension". Also removed was "Detail BB", what ever it was.
Taking a WAG, the installation details for bows 2, 3 and 4 did not change, so the "Extensions" (aka "adapters"?) were used on the first bow.
That being said, it's now a "How to" assembly referral from another 64 Hardtop.
Jim