How did you feel when you did the 12.5 mile ride? Was pain an issue while riding? If so, where? Was it the same bike? Do you have pain on the stationary bike?

Any pain is bad. Muscle soreness is ok, and part of training. But for pain, the best route is getting a bike fit, and PT/professional advice, rather than advice from here.

I have knee and shoulder issues/surgeries, and have done both PT and gotten a bike fit. The bike fit wasn't needed until after I hurt my knee, but afterwards made all the difference.

Personally, I find it much more rewarding/energizing to ride outside than at the gym. Much better scenery. I would think that just getting out and riding would be better, but still do cross-training (core work, etc). As long as you stick to short rides you can do with good form, and without pain.

I was at a much higher weight than you starting out, and very unfit- riding even 1 mile was a challenge. I would ride 4-5 days a week, and designate Saturday as my "long ride", which got a little further almost every week. I remember at first I would bring a lunch and a book, and take a few breaks while completing a 3-4 mile ride. Soon, I would only need 1 break riding 10 miles. After 6 months or so I was up to about 80 mile rides. I've gotten in and out of shape a few times since then, and find that just getting on the bike and easing into it works best for me. You can start at an easy speed, on flat ground, and gradually add speed and hills if you want too, just start getting your body on the bike (if it doesn't hurt).