Do you recover before magic mile?

You could pause the watch at the end of the 4th acceleration-glider drill to have a rest (or get to your starting point) before the magic mile auto-starts. Or, you could choose to totally skip the acceleration glider drills by pressing the lap button 4 times (1 for each drill). I don't think the training plan really cares what your moving pace is during the acceleration drills, or how long you spend in that step. It's not as sensitive of a training plan as you might think.

Personally, I would view your tiredness as a sign that you are breaking into new territory with your fitness and pushing your limits a bit. As you continue to push your limits, your body will get stronger. I am not a fitness coach, but I don't think you should be disheartened by 45 seconds in a training mile. As long as you don't have any unusual pain, you are moving in the right direction.

Thanks for that response. I did start to take extra time, but felt like I was cheating. I've only been running for about 18 months now and am still learning to not be so black and white about things.  Seeing progress keeps me motivated so it just felt like a step backwards when the time was lower than before.

I've gotten to the point where the gains are now incremental and not leaps like they were the first year of actually doing something after 25 years of being idle and I'm trying to adjust my expectations. 

No pain, so I'll just keep at it and keep pushing.

When it comes to the Garmin coaches, I try to use the tool and not let the tool use me. So if I'm feeling good and want to push things, I'll let it beep at me for going faster than it decrees (within reason). If I'm not feeling it, I'll modify the workout. But it doesn't seem punish you for deviating from the plan unless you start to skip multiple workouts.
From my experience, I see the most gains when I make myself do the race pace repeats, speed intervals, and hill work consistently. All the parts that aren't as fun or relaxing, but oh well.

I totally sympathize with the "seeing improvement as motivation for further improvement" perspective. It's disappointing when you don't see improvement with each point of comparison. To your credit, when I got back into running after 10 years off, I wasn't interested in tackling a 10k race plan for years. One particular 5k I run every year, I have dropped a minute off my time, each year, over the last 8 years. I first ran it at 29 minutes, and last year I was 21:39. So your fitness base building over time is part of the bigger picture, and these magic miles will be totally forgettable in the long run (no pun intended).

I found that Jeff Galloway's half marathon training plan suited me, and I ended up running 3 halfs last year. Good luck to you!

Thanks for all the perspective and encouragement. I don't think I'll ever race as I think it may consume me and at my age, I'll probably hurt myself doing too much. I compete with myself and so far it's been good and I've grown to enjoy running even though I hated it when young and only did it as a requirement for sports fitness.

I find Jeff's plans are good for me too; I've yet to complete a full half marathon plan  because I get bored once runs become longer than 8-10 miles so I usually stop, do a month of mostly easy runs (with some stuff learned from the plan sprinkled in) and then start a new plan.  Jeff's motivates me more because I don't dread them knowing there are "walks" to break stuff up, especially when it's hot and humid.  When I first got going I used Nike Run Club and it was great and taught me a lot starting out. I started not being able to even run a 5k, to doing it in 32 mins to under 30 and am now able to do it in just under 23 min and have gotten my 10k to under 50 so I'm super happy, but I'm trying to keep motivated to not get complacent and stop. 

Again, I do appreciate your insights, motivation and perspective, it's good to get as I don't really have anyone to bounce things off of.