I’m sure the pros will give you a detailed response but I can help with some of your questions based on what I’ve learned from the 2 books and this website/forum.
1) It does sound like your AeT is lower than the formula suggests. The MAF seems to correlate well for most people with a history of endurance training but tends to over-estimate the AeT for others. I am one of those people without a long history of structured training so I can maintain nose breathing for at least 10-15bpm above my AeT that I’ve confirmed with a lab lactate/gas test and a 60-minute treadmill test. I’d recommend redoing the treadmill test using the standard protocol of a 15-minute gradual warm up followed by 60 minutes of constant speed/incline. Take the ratio of the average HR from the second half of the 60-minute test to the average from the first half. If the ratio is greater than 1.05 (5% test), then the HR you noted at the very beginning of the 60-minute test is above your AeT and you should redo the test with a lower starting HR.
2) Early on, I’d be cautious with your total volume of training even at or below the AeT. Your body needs time to adapt to the training stimulus and doing too much too quickly can have a negative impact on your performance. Stick to the plan early on and see how your body responds. Once you get a feel for this response, you can try experimenting with higher volumes and how they impact you.
3) I’ve read that most people have problems with the L-sit, and I did too. It really is a matter of time and consistency. I was unable to get off the ground even with crossed legs. After several weeks of consistent core training, I got to the point of holding crossed legs off the ground, then short bursts of straight legs, and now finally I can hold the L-sit for ~10 seconds. The other core exercises will strength your core obviously, so just stick with it and keep trying the L-sit, it will come.
4) There is a very in-depth discussion on this in the books. I believe it boils down to the fact that it takes a relatively long time to build up the support systems for the aerobic energy pathways whereas your body quickly takes to the glycemic pathway of anaerobic training. I am far from an expert on this so I’d recommend the books for more info or Scott J. may chime in on here.