Congratulations on the amp. You built the original, 2 power tube version so I’m wondering if you got the updated construction info that DH put out about the Two Stroke design.
Does the MM OT have the same specs as the Hammond 125ESE transformer that is spec-ed in the book? If so, you can use the table on page 188 to help you select the correct secondary winding to use with each power tube / speaker load combination. If not, you can use a turns radio formula to calculate the correct load for each secondary lead depending on the primary input impedance. The OT can stand some degree of impedance mismatch so don’t get too worried if the secondary impedance does not exactly match the load. Fender gets away with 100% mismatch without issue. You can put the output tube in either socket, your amp is a duel-single-ended design which means that the tubes are on and working all the time (unlike a push-pull design) so it does not make a difference which socket you use. Don’t use two different tubes at the same time though. In fact, the only 2 tube configuration you should use is 2-6V6s. My favorite is one 6L6.
What “problems” did your tech find with the layout? Which MM transformers did you use?