So the track work does increase in distances and then varied paces. Sometimes they are run at 5k pace and others at 10k pace.
Absolute guarantee that if 9 min/mile is in fact "I" pace and is your defined "10k" pace, then you do not want to go faster to the "5k" pace. That would put you in the true sprint type workout and should be no more than 40-95 seconds in total duration, the RI on those would be like 2-3 minutes too. How does that line up with future "5k" workouts he prescribes?
I think our thought process was to gradually work to shorten the time to complete the 400m each week but again we are sort of just winging it and today was a bit but a guess at what to run these at.
I would suggest not doing that. The benefits are found at that exact pace (what "that" pace is we're still trying to figure out). Is it possible for you to do 2:10 or 2:00 400m instead? Sure, but the benefit/recovery structure changes completely from them and may do more harm than good.
This was definitely not a terribly strenuous run. It maybe pushed me a bit harder than our normal maintenance run pace where we do 2:00/:30 intervals but not exceptionally so. Again total mileage only ended up at 3 miles but I definitely still had gas in the tank.
Definitely something we discussed in the past, but I do think you must have superior speed (high VO2max) than most. You're really good at the "sprint" workouts and thus have gravitated towards the run/walk. So it's possible that you're pacing spectrum is shaded heavily towards the faster workouts. You can go fast, but have trouble maintaining that fast over longer durations.
That 2 minute threshold is super important for the I paced runs. Because the run uses mostly anaerobic power up to that point. But beyond 2 minutes is where the aerobic system gets pushed really hard. So I'd be interested to hear how a 3 min or 4 min run would go at the same pace. Because that's when you're holding VO2max for a long period of time and it pushes you hard.
If you don't find the longer duration at 9 min/mile incredibly difficult, then I'd venture to guess that the 9 min/mile may in fact be closer to 10k pace than 2 mile pace. It sure makes for an interesting experiment.
As you progress with these runs, I think the #1 thing to watch for is the fade. If you fade at the end of the workout - 2:15, 2:15, 2:15, 2:15, 2:20, 2:25, 2:30, 2:30 then it's a sign that the workout is too much.
For me, I always try to walk the line of improving with benefits, but minimizing the injury risk. If this were me, and my goal was a 2:15 HM, then I would run the 9:49 min/mile paced 10k workouts and 9:25 min/mile 5k workouts for a few weeks. If after a few weeks, you still find them not so hard, then I'd move it up. This would be the safer choice and lower injury risk. You might lose some benefits with the slower paces if they're not appropriate, but if the faster paces aren't appropriate you could place yourself at a much higher risk for injury.