I'm 6'4" and my instructors are shorter than me. All my students, but two, have been shorter than me. The two that were taller were 6'9" and 6'11" respectively. KunTao Silat has some very low movements which are worked on for protracted periods of time that yield real benefits in conditioning and application when proficient with them.
Excellent advice to never place your knee in front of your toes. It's just good structure and if you start working hard and long at low movements or squatting with weight it will save your knees.
That said, I squat lower than all of my students for longer periods of time. The vast majority of the time, unfortunately, it is simple conditioning. As an earlier post stated, "Keep at it." You need to build up strength in your muscles, tendons and ligaments in your legs and knees. It will get easier over time, but will take awhile. If you are experienceing sharp, knife like pains at certain times instead of the burning, "Oh this hurts and I'm tired" pain, go see a physician and get checked out; you may have some real structural problems that need to be addressed. However, it's unlikely or you would have bumped into that type of pain already when first attempting the movements, and the pain gets worse through use over time instead of better as in a conditioning matter.
Two of my students are about 5'7" and my stances are about 8" to 10" shorter than them while moving while I continue to tell them to get lower. An old familiar line to many people I'm sure. There is a purpose for it other than conditioning and explosiveness in application which will become clear as you rise in experience. That said, it's not realistic to assume that someone my size will move like someone 5'4" in low stances. The physics simply isn't there, but I do work and keep trying. It really assists in a multitude of ways. I've been told due to my size and conditioning that being able to move fluidly and low with proper structure usage and application makes for a very difficult to handle combatant.
Best wishes, and keep at it.