Some suggestions (though having one PT session would be the best!):
Warm-up thoroughly, so that the knee joint has plenty of circulation going before you start the main workout. 10 minutes isn't out of the question. Also, gradually work into a bigger ROM, starting shallow in most moves.
Try to reduce inflammation. You can do that by icing the knee right after a workout. Also,, "Blue Mangosteen" (which I get from here:
http://www.oneluckyduck.com/index.asp?PageAction=VIEWPROD&ProdID=207 ) is an excellent anti-inflammatory made from dried/powdered mangosteenn and Klamath Lake Blue-Green algae. It takes a while to work, but it does seem to work well. I've been taking it daily (the contents of two opened capsules in a smoothie) and I notice the difference when I skip it for several days. Eating antioxidant-rich foods and avoiding too many acid-producing foods (animal products, most grains, most nuts--except almonds) can also help with inflammation.
Making sure that the muscles around the knee are balanced in both strength and flexibility is important. The vastus medialus (the "teardrop" muscle on the inside of the knee) is often a weak link.
You can strengthen this and other muscles by doing 'quad sets': sit on the floor with legs straight (either prop your uppper body up on elbows or lie down, whatever is most comfortable). Bend one leg and keep the other straight. Tense the quad in the straight leg, keep the knee locked thoughout the move, and lift the leg under control until the knee is about even with the knee of the bent leg. Hold for a count of two, then lower under control. You can target the VM more by turning the toe of the lifting leg out to about a 45-degree angle. After you work up to sets of 15, add a light ankle weight.
If your knee hurts too much to do that, you can do this alternative exercise: in the same position, but with a folded towel under the knee of the straight leg, press down into the towel to activate the quads.
Also, make sure to stretch all the muscles around the knee, especially the hamstrings, hip flexor and IT band.
You may want to look into your biomechanics when doing lunges, since that's the exercise that gave you trouble (and obviously it was because something was not right). Make sure the knee doesn't buckle in, keep the knee back of the toe. Once you get back into doing lunges, it may help to stick with static lunges (even while holding onto something for help with balance and form) and/or doing lunges with the front foot on a 4-6 inch platform).
Also, as a general rule, if it hurts, DON"T DO IT!