Hi duggski1,
I have had a similar problem as you. For whatever reason, it's tough for my fingertips to build callousses. But the more I practiced, I was able to withstand the little bits of pain better. I also started with a Squier strat and I've had that issue happen to me too, where I would constantly hit the middle pick up.
It's best to adjust your picking hand if you're having trouble hitting the knobs and the pickup. Going for a Gibson-style guitar like the Epi SG should solve those problems, which is a great choice.
As for your fingers, it's all about practice, my friend. I always suggest guitar learners to start slow, and not get too crazy. That way you learn the right way and you won't build bad habbits down the road. I hope that helps somewhat. I've been in your situation before and eventually you'll get the hang of it!
Best,
Billy