"So they brought me down on my knees and had me throw some long toss and whatnot and truth be told I was throwing about 150 to 200 feet easily on my knees"
All this says is that you have a strong back/shoulder/arm, which is a good thing. Are they trying to say you can be faster? Or more accurate? Just the jist of your post, kinda says you possibly don't use your lower half as efficiently as you could, plenty of drill work out there to let you know how to improve your delivery efficiency, remember the deal is timing and posture, so no quick fix, just hard work and dedicated effort. Step behinds are great for getting you to concentrate on posture and knee lift (Start behind the rubber with both feet together..modified stretch position, take the back foot behind you to the rubber position, this will get you in a good posture position when you knee lift, your hips will be in proper orientation, you will be stacked properly posture wise and your momentum will be moving towards the plate...now from knee lift to footstrike you need to do basically 3 things...get your hips moving toward home, your pitching hand around and back up to the power position and front hand in front of you thumb down...get all this to footstrike and you are ready to utilize the lower half of your body in your delivery...repeat and incorporate this into your bullpen for a while and you'll find a whole lot more control and velocity in your motion..I bet).