I've had two emergency sections. First, for twins, was grisly but I was back to 90% after four weeks although didn't start running until about 12 weeks post-section. The scar line had adhesions and 'pulled' on occasion, and in wet or damp weather it could feel twingy (weird!). Other than that, all okay.
Second time around I took things really slowly. I scarcely left the sofa, didn't lift, didn't do too much. In short, I did everything to maximise my recovery. I still felt bloody awful and no better by 4 weeks post-section, which I'd been holding out as my 'recovery benchmark' from last time. I went back to A&E a few times, saw my GP and even had abdominal ultrasound to check for any problems. Nothing, they simply said I was 'overdoing it' or may have had nerve damage.
At 6 weeks I suddenly developed a temperature, rock-hard abdomen with a big, red, hot raised area around my scar. Turns out I'd had an infection bubbling away in there for 6 weeks which had finally flared up. It wasn't in the scar, which had healed fine, but deep in the muscle/underlying tissue. Ironically, had I not taken things so easily and 'overdone' things a bit it probably would have flared up earlier. As it was, I ended up in A&E & got a massive dose of antibiotics. The infection cleared and I felt fine within a week. It made a massive difference. And there was I thinking and being made to think that it was all in my head; that I was being a bit of a drama queen about it all. Aside from the relief at finally getting it bloody sorted and feeling halfway towards human again, I remember thinking "I knew it!". I knew it had been more than I thought or was told.
I'm not saying you've got an infection at all but I am saying that if you don't feel right then go and see your GP or ask to see a consultant at the hospital. They can perform an ultrasound scan and do some blood tests. They checked me for infection via blood test on a couple of occasions and said I didn't have it, but as a (finally) switched on doctor pointed out, when it starts showing in your blood then things are at a different stage. It doesn't always have to show up on blood tests for it to cause debilitation and pain. Certainly I was side-swiped and scarcely mobile at 5 weeks post-section when I still wasn't presenting 'infection' in my blood tests.
I do think 3 months is a long time to still be feeling shit and in pain. Twinges are normal as the muscle heals, but anything more should always be checked. Is the pain a burning sensation? This can be nerve damage, which standard painkillers won't help (you need neuralgic 'painkillers' - usually micro doses of anti-depressants). It will pass as the nerves heal again but it can take time. Either way, go back to the doctor and tell them you don't feel right. Be specific and detailed and forceful about the degree of pain. If it helps, keep a 'pain diary' for a couple of days beforehand. Write down when it hurt (& what you were doing at the time, if anything) and how it felt (burning, achy, sharp, pulling, tender).
Hope this epic reply is of some use. Congratulations on your baby!
You will heal. You will feel normal again.