they're roughly along the lines of "This is gonna hurt" or "Ow" or "Yep, that was painful"
I'm not a therapist or an expert, but I think you need to dig deeper. Why are those thoughts coming up, of all the (true) thoughts you could be thinking? I would guess that there are supplementary thoughts to those, ones that magnify or exaggerate them, like "This is going to be too painful" or "That was unbearable."
What sets those latter two thoughts apart is that they imply that the pain is somehow excessive, which (if true) would justify stopping. But whether the pain is "excessive" is kind of fudgeable by whichever side of your mind wants to quit. (Of course there is such a thing as excessive pain, and pain could be a legit sign of a problem, as /u/memoridem has pointed out.) If thoughts like these are underlying and giving strength to your urge to stop, try to figure out what exactly you mean by "too much" and see if the "too much" claim is really true. Then if it's not true, formulate a response to memorize.
Why are those thoughts coming up, of all the (true) thoughts you could be thinking?
At a guess, it could simply be because pain /hurts/, and I live a comfortable enough life that before I started this exercising thing, I haven't had to worry about anything worse than a headache or cat-scratch or the like for years. The other day, when I was doing 24 push-ups in a row instead of 5 groups of 5ish, by the time I hit the last one, I'd call the pain level at least on the order of magnitude of the migraines I used to get or the time I got a nice hospital-visit...
"Cryonics has a 95% chance of failure, by my estimation; it would be downright /embarrassing/ to die on the day before real immortality is discovered. Thus, I want to improve my general health and longevity."
That thought has gotten me through three weeks of gradually increasing exercise and diet improvement (I'm eating an apple right now) - but my enthusiasm is starting to flag. So I'm looking for new thoughts that will help me keep going, and keep improving. A few possibilities that I've thought of:
Pride: "If I'm so smart, then I should be able to do /better/ than those other people who don't even know about Bayesian updates, let alone the existence of akrasia..."
Sloth: "If I stop now, it's going to be /so much/ harder and more painful to start up again, instead of just keeping on keeping on..."
Desire: "I already like hiking and camping - if I keep this up, I'll be able to carry enough weight to finally take that long trip I've occasionally considered..."
Curiosity: "I'm as geeky a nerd as you can find. I wonder how far I can hack my own body?"
Pride again: "I already keep a hiker's first-aid kit in my pocket, and make other preparations for events that happen rarely. How stupid do I have to be not to put at least that much effort into making my everyday life easier?"
Does anyone have any experience in such self-motivation? Does this set of mental tricks seem like a sufficiently viable approach? Are there any other approaches that seem worth a shot?