I think you definitely shouldn't get lifting advice from chiropractors
You should never squat with your feet INWARD. I don't why someone would come out with something like that. Squatting with your feet straight ahead is great if you have the flexiblity to do it but chances are that could just be worse on you knees due to lack of depth or changing the mechanics of it. As long as your knees line up with your feet I don't think that has anything to do with patella tracking issues.
The idea of doing step-ups, etc. is to help adress that. Also squatting nice and deep is thought to have benefit. That and the PC work for hams and glute....this all has to do with the VMO and the idea that you can selectively isolate it a little to take care of the imbalance that is thought to occur commonly. I don't know whether you really can but I have found great benefit from step-ups, single leg stuff in general, and lots of PC stuff like pullthroughs, etc...
I talked to you before about the mobility issues, correct?
I certainly think RDL's are a fine idea. These days, at least among the guys I follow, extensions would no longer be the preferred choice if it is patellar tracking issues. If you do do them, do them light.
Try an illiotibial band stretch as well.
Other than that I don't know what eles to say. Sure wish I could be of more help.