Marshall,
Please don't take this wrong - several people, including myself, have asked you for a schematic on the last thread and this one as well. Nobody has time to sit down and go through your pics to check values and many connections are just not visible. There are folks here who would like to give you a hand, but you have to "help me, help you!" Any advice we can give is a shot in the dark without a schematic that references EXACTLY what you have. Here is just one reason why... You mention over and over that it is a clone, but some values you are giving are not close to a Major. Please, if you were not provided a schematic by the builder, draw one out, or use the original 1967 (that has been fixed) as a guide and fill in the blanks. Check and double check the values and connections. This will also help you with your understanding of the amp.
Ed,
I don't think you can get an off the shelf tranny with other than 40% taps. I don't think that is the problem here. The flyback issues that you mention were inherent with the Major are the same with EVERY UL amp. The problem with the Major was the crappy OP transformers were not up to the task of absorbing these transient spikes during overdrive conditions.
Jim