Good, this is progress. I looked on the internet for a picture of the MT12A components but I couldn't find one. There is a poor quality picture of the MT12 here
http://www.hitaudio.com/Products/MT-12.htm. It seems to use the same power transformer. Can you confirm the wiring connections to the transformer are the same in your amp as in this picture ? If they are then here is a sketch of what I think the transformer connections are (but please remember I am just guessing - you must follow the wiring in the amp to confirm this)
Looking at your measurements
PRIMARY: In your final photo you say you are measuring the primary. How do you know this ? Did you follow the wires from these terminals back to the mains supply ? If you did then the wiring to the transformer in your amp is different from the wiring in the MT12 internet picture. But actually I think you are measuring the heater winding in your photo. You are using the 'continuity/diode test' range on your meter. This will confirm continuity but it will not tell you the resistance. A resistance measurement would be more useful. The result should be very low - probably less than 1 ohm. To get an accurate result you must subtract the resistance of your test leads. Connect the lead tips directly to one another and measure their resistance. Then measure the winding resistance and subtract the leads' resistance to get the true winding resistance.
SEC1, 2, 3: Can you take some photos of the connections you made to the transformer when you took these measurements ? Otherwise I cannot really be sure which windings you are measuring here.
If my sketch of the transformer connections is correct then the primary windings are at the bottom of the picture. You should reconnect the red jumper wire between the two 115V halves of the primary then measure the resistance between its ends i.e. from the Brown wire terminal to the Blue wire terminal.
Then you should identify which terminals on the right hand side are connected to the bridge rectifier. I think this is the HT supply rectifier. Is this correct ? If it is then can you measure the resistance between the transformer terminals to which these two red wires were connected. It's possible that the HT winding was in more than one section, like the mains primary. If it was then you need to reconnect any jumper wires which linked these sections together before you measure the resistance.
You should also make sure that there is no connection i.e. open circuit between the mains primary winding and any other terminal on the transformer and also between the HT winding and any other terminal. If there is then the insulation inside the transformer has probably failed.
I cannot see any other connections to the transformer, but there may be some. The front panel display, for example, must be powered from somewhere. Can you tell me if there are any other connections ?
VB
