Here's what happens to your body if you're an overweight unfit white 30-year-old who suddenly starts cycling a lot. Or at least it's what's happening to me right now. I don't feel like I've lost weight, but am unable to check since I haven't seen a scale in this country since this trip began. My lower legs seem thinner than they were before, and the muscles look about the same size as before the trip. Everywhere else I'm still fat :S. My hands have developed peculiar calluses between my thumb and index finger, with a little slit inside of them that looks like they've been cut, but the slit is not nearly deep enough for that. The finger-side of my thumb's joint but has gotten thicker and more callus-y as well. Lower palm area feels a bit sensitive and slightly harder than normal, but not much.
In terms of muscle aches, it's mainly the knees. My knees are in a state of constant pain, yet not quite pain. It's not as if I've sprained anything, nor does it feel like the times I seriously hurt my knee my climbing too much. Instead it appears to be a standard muscle fatigue that doesn't really inhibit my ability to cycle or walk. It's been fairly constant ever since the mountain stages. Sometimes my back hurts slightly from being in the cycling posture for too long, but I tend to take frequent breaks and stretches so it's usually gone by the evening.
The areas around my temples and of course my nose was completely covered in sunburn for the first week or so, but is finally, slowly, starting to normalize. It's still red and the skin is quite wrinkly, but I no longer seem to be as strongly affected by the sun as I was before. Probably thanks to the new SPF 50+ waterproof sunscreen as well. My arms are still flaking from the very first day during which I didn't put on any sunscreen on my arms. Every single day after that I've been wearing long sleeves..
Warning: butt part comes next! My butt has firmed up a lot and seems to have adapted to the saddle. I no longer lose sensation in my nether regions when I cycle, despite the saddle angle being shallower than I've previously had it set to. I can cycle for 30-50km without any discomfort depending on the road conditions and how much I've cycled the previous day. After that it still hurts :S. But at least I'm improving.
Things I would do different: try to use that softer gel saddle again and try out more positions. I'm sure there's some way that I can make that thing more comfortable than what I'm sitting in now. I'd also buy a better hat that offers shade around the entire area of my head. SPF 50+ right from the start was an absolute must, I should not have trusted the shitty SPF 30 one from Spain. Finally, thicker and more robust cycling gloves would have been nicer. My current ones are already falling apart and I've only been using them for 2 weeks. Bottom (har har) line: don't worry about your body too much, it can adapt to physical situations easily, but worry about the sun and adequate protection.