Jack:
Thanks for writing in with your questions. Hope the following helps.
I would recommend that you do the AeT and AnT using the same modality rather than one running and one skinning uphill. I also recommend that you use the starting HR not the avg of the first half as the denominator. Since you didn’t have much drift this will probably only result in change of a a couple of bpm.
1)You are correct that these are insignificantly small differences between tests and could be due to fatigue or even differences in treadmills. But you can probably count these results as valid on the day.
2) Yes, I would have expected that in 9 weeks of 6.5hrs/wk of Z2 training you would have seen a change in HR drift. Was the speed of the belt the same? If you were moving faster that in itself is the actual goal and would indicate the even with the same drift your aerobic capacity ha increased.
3) if the answer to 32 is that the speed was the same then your suggestion to increase Z2 volume/week is direction I would recommend you take. 4 months lay off is a long time and it may just take more time to move the aerobic needle. However it seems like you are experiencing good results in the mountains. A 20 mile run is nothing to sneeze at. Were you able to recover pretty quickly from that? Real world performance and your perception counts for a lot in assessing fitness gains.
I know this is not a black and white answer but I wish you luck. Clearly something you have been doing has been working. So don’t loose faith.
Scott