Oh these kind of fluxes will happen through-out your whole journey. Our bodies are amazing at adapting to what we do to it. One of the reasons we do so well as a species, our adaptability and endurance. PLEASE remember that last point as I will come back to it.
Your metabolism is going through a crash course of what is right again. Cutting the "crap" out of your diet is allowing your body to "normalize". Eventually it will plateau to the point you wont see any gains or losses, this will and can happen through your whole journey. There is a reason weight lifters don't ever do the same reps, with the same weight with the same tools their entire lives. Runners will never consistently run 3 miles when training for a half marathon as the body gets used to 3 mile runs and halves are worlds apart. Eventually your body will get used to these workouts and they become a normal thing and will stop producing results. The amazing thing to this, is we use this adaptability to "Keep the muscles guessing" because as stupid as that saying is, it is true.
The rate in which you change workouts, and output is 100% dependent on you and your body and what your goals are. Just as diet, no one can tell you what will work for your body as it will do what it does best. Adapt. Eventually these plateaus will become easier to notice and correct. All this just takes time and experience as no one can tell you the exact moment all this will happen to you.
Now for the endurance. You must understand your body can endure some shit, a lot of it actually. Ask anyone who has done a triathlon, decathlon, ultra-marathon or a regular marathon. The more you put your self through and the better you learn of your own body the more you will find your self capable of doing. The 4 examples I listed, those guys started somewhere between shit and "A good runner". The pain you feel throughout this entire process will suck, however, it is not going to kill you or cause long term damage (As long as you know your body). Its easy to say here on SSRCG forums, but it really is not that hard. When you understand what a build-up of lactic acid is, or how you obtain muscle failure, or how to improve your O2 intake, you realize how to look past the pain, fix the pain, or adjust your comfort levels.
Just remember your body will adapt to what ever and where it is going through. However, its designed to be durable and we have the highest endurance and psychological commitments than any other animal species out there. Dont get upset with a lack of results or change, just take that challenge as your body playing chess with you.
I also have some tips/tricks/helpful thoughts regarding metabolism and to help maintain high levels if you want me to jot those down. Im sure Gav can get into nutrition and regimes for what you need to do for what. I am more interested and involved in learning about the science and mental aspect of training so can chime in on those aspects.
Just remember, everyone offering you advice and those that push their ideas and thoughts as fact can be right and most likely are. However that is only because they are discussing their bodies, and because they are that self aware of their own bodies they know what works. Their faults are in not understanding everyone's metabolic rates, hearts, lungs, muscles, bone structure is different. You need to find out what YOUR body needs. Ofc take advice, try ideas and just be smart.
Right now? You're on the right path. Fix the diet, let the body adapt. Once it has "normalized" start the work. Once it has "normalized" again, change the work. Once you hit a point where nothing is working, dive into the science, dive into the supplements, dive into what ever other crazy fad you want. Just remember your body, your rules.
Keep up the work though, I love seeing shit like this. Self motivation and determination are boner material.