"I'm not a PT, I just play one on television."

It might be a good idea for you (Flatlander) to get a referral and a script for PT.

Open chain quad work is pretty much not the best choice (watch me dance around to avoid saying "fer gawdsakes, don't do that!") for post-ACL. Open chain is when you are firing off your quads in a non-weightbearing situation. (straightening your knee with ankle weights on, doing quad extensions on a quad machine)

Closed chain quad work is peachy. (leg press machine, squats) That's where you are using your quads while putting weight through the soles of your feet. Just don't bend the knee more than 90 degrees while weightbearing, at least until you get the all-clear from a PT.

For the hamstrings you want to do both open and closed chain work, and you can bend more than 90 degrees with that.

You really need someone to look at your firing pattern before you start adjusting your bike.

It's probably not the best sign in the world that your "bad" hammie is smaller than your "good" hammie. You need those hammies!

Doesn't matter how long ago you had your incident, PT now is cool. Depending on the laws in your state and your insurance, you may be able to go to PT without seeing the doc again. Try calling the ortho's office and ask if they can fax a script to a PT clinic. (ask around to choose a clinic) Sports therapy/ sports PT might be the best choice, if you have a good sports therapy clinic near you. They will have a good handle on the running and biking part.