I am sorry to hear about the injury.
A lot of it you will just have to experiment with on your own. You could...
1) Look into bodyweight work (1 legged squats, wall sits, that sort of stuff). How about all the funky type stuff that you see on sites like dragondoor/mike mahler's type stuff (he has a site).
2) Hacks? If you can deadlift, you may can hack.
3) For hamstrings frankly, you should be set with all of the ideas off of westside barbells site, namely elite fitness systems. They are all over core strength and training glutes and hams. Reverse hypers, glute-ham raises, pullthroughs, yada yada.
4) Maybe try lightweight box squatting and see if that takes enough pressure off knees.
I tried to go without all types of squatting and leg press for awhile and I really didn't come up with anything great. Lunges worked okay for awhile, but they are just an inferior version of the squat in many ways. But my temporary problem was lower back.
For knee problems, I am most inclined to want to try Westside stuff first and foremost. They tear shit up all the time and seem to come back squatting strong enough.