The biggest thing I can say is to be careful and aware of what you do to your "good" leg. Since my amputation (on left side as well) I have built a great deal of strength in the "bad" leg, but mechanical differences alone cause the strength level to be a percentage of what the other leg is. Given where my residual hits the socket on the pedal stroke and those differences in strength I would guess that I do about 75% right leg/25% left. One of the most important aspects I have found is to keep doing stretches that are possible, particularly to the IT bands, keep my knee wrapped when it's even a HINT of cool out, and to be in a super low gear on takeoff so as not to "twinge" my knee getting started.
My recurring issue is that when I ride a lot (which has been about a year) it tends to pull my hips out of alignment and causes some pretty severe lower back discomfort. The stretches help but it does turn into a trip to the chiro from time to time.
As to going to see a doctor or specialist about it....my thoughts are you will be paying someone to tell you the obvious. If the muscle group is gone I don't see what physical therapy is going to do about it, and likely why they didn't send you. As to the flexibility issue I would suggest checking YouTube (etc) first and see if you can find some stretches that work for you. Consider perhaps a yoga class or the like? Hard to say as I physically cannot do many of the stretches and exercise routines that would help with my flexibility issues.
You will certainly face future mobility issues. You will face future issues in your good leg simply due to the increased wear and tear you are putting on it. The option is to "stop living", which really isn't an option at all. No point in sitting around waiting for what will happen to happen. Deal with it each step of the way and devise ways to overcome it, if you can.
All in all, best of luck to you and keep at it.