You guys are combining bodybuilding mentality with strength training mentality and thus confusing me greatly.
Are we talking about training movements are training bodyparts? Pick one. Combining the two modes of thought will always give you a hodgepodge.
Some general suggestions for your knees based on what you've said and a lot of assuming:
Do more posterior chain work. Lower the volume on deadlift and then supplement that with more pc work like romanians, pullthroughs, the aforementioned glute/ham raises. This is to strengthen the hams and activate/strengthen the glutes as I'll bet you are quad dominant. Pullthroughs, imo, would be the best thing to start with.
You'll want to work on hip mobility and check on ankle mobility.
Lack of hip and ankle mobility are actually the two main causes of most knee problems.
You should try stretching the hip flexors and quads a bit. Foam rolling for both of them would be a good idea. You'll probably want an iliotibial band stretch (itb) and a piriformis stretch. As well as foam roller work for the ITB and TFL. [ info: http://www.t-nation.com/findArticle....4-021-training
Work on lumbar stability. Activating and strenthening the entire core. Do planks and other stability exercises.
Work on thoracic mobility.
For single leg work don't go straight to bulgarian squats. See if you can do static split squats. That is basically a bulgarian without the back leg elevated. Work on keeping the torso staight and the knee in line. Pick a stride length that feels good and see how you do with that. If you can't do that with movement try a split squat isometric hold. DROP THE LEG EXTENSIONS. They are probably doing more harm than good. Don't do leg press as this will just further the imbalance.
You can also try step ups.
Wolf is correct in suggesting you may be able to box squat. Heck, depending on the nature of your problems you may do better with front squats rather than back squats. But you may want to address some of these other areas first for a while. As he mentioned you have to evaluate whether you are donig those things which cause you pain CORRECTLY. Maybe if technique was corrected certain pain causing things would no longer be a poblem and those may be some things that would help to correct the imbalances. That's always the thing to check first before you just choose different things....
For more info on these kinds of things check out Mike Robertson and Eric Cressey. They will also point the way to other names to look for. Mike Boyle for instance.
Yes, all this has to do with knees