You've got some "Lydiard" elements here but there are, as Chris and Glen mention, parts that are missing. And one of Arthur's ideas was that after you've done a certain kind of training for a while you max out on its benefits and should move on to something else. Anyway, here are some thngs about your training that I wonder about.
There is, as I mentioned, not a lot of variety throughout the year if this is what you do 80% of the time. I'm not sure if the switch to things like the 12x400 is part of the 80% or if that's part of what you do during the other 20% of the time.
I assume that you know that you aren't following the "classic" periodized approach, i.e., there's no specific base phase, hill phase, interval phase, etc. That's OK, when Barry Magee was coaching me we didn't follow the classic phased approach either. But we did have some hill sessions, fast relaxed strides and time trials in the mix. I think you could benefit by switching some of the tempo runs or cruise intervals to hill sessions.
I also think you could benefit from a base phase, where you just do the miles, even if you aren't going to follow a phased approach during the rest of the year. Barry had me do a 10 week stretch like that each year and it always seemed beneficial.
Another thing I wonder about is whether you've become sort of a slave to the watch and are wearing yourself down. When you're hitting those 5:20s in your tempo runs is it because you're consciously aiming for those paces or are they by-products of just having a run at a respectable effort? Is the latter part of the run feeling harder to manage than the earlier bit is? On the long run, do you run faster in the second half because that's what happens normally or because you're "making" it happen?
There's a lot of information in your posts but there's also a unstated. With not anything more to go on, I would suggest the following:
1. Toss the watch. Just cover the distance but let the pace find you. If you run by time and not miles check the clock on your wall or in your car at the start and end of the run just to see how long you're running.
2. Have a break of about two months from any kind of "effort" running and focus on comfortable distance. Note that I did not say SLOW distance nor did I say FAST distance. Do the distance at whatever pace works but be sure you've got enough left in the tank at the end so that you could run a bit longer if you wanted to.
3. After the distance phase, go back to the mix of tempo runs and intervals but add hill sessions and fartlek. Spread that mix out over as many weeks as you need to allow for recovery from the sessions, i.e., don't worry about fitting all of them into a week or two and don't worry if you've had a couple weeks without doing a certain kind of run with the exception of hills. Get in a weekly hill session once you come off the distance phase. Continue to stay away from the watch, just run at what feels like a decent yet manageable effort.
4. Remember that this advice may be worth exactly what you paid for it.