I agree with squitdad that you need to make sure the bike is set up for you to pedal efficiently and use the mechanics of your legs properly. It may be a sit-up, leisure type of bike, but you still need the right seat to pedal distance for good(fun) riding.
Also, do away with the squats with free weights. Your knees will thank you when you are old. Getting into that kind of weight lifting without a good trainer present is asking for trouble.
In fact, you said that you had just started a new phase of training that included these squats and that you tend to over do squats and it hurts to walk the next day!. I would guess that you strained some muscles doing squats and they have been trying to recover ever since, but you don't let them. "It's not unusual for me to overdo the squats or whatever, and then barely be able to walk the next day" That statement leads me to believe you really need supervised weight training. You are hurting yourself and you can do long term damage.