Well guys I figured mine out and I am willing to bet you that your issues may be stemming from the same thing.
On the switches that do work (excluding the master switch) such as the passenger side lock or window or the rear seat window switches. Pull one of the switches that do work. Look on the back of it and see how many metal "prongs" there are on it. Now pull the switch that is not working and count how many prongs on it.
Turns out my stock switches had one less prong on the back (#5 to be exact was missing, you have to look to see the #'s engraved in the plastic)and the switches that by blue LED's were soldered onto (I have 2 sets of complete switches) had a prong coming out of the #5 prong. So what I did was clipped off my blue LED from the switches (switches that had prong #5) and clipped off the green LED from my stock switches (switches that did not have prong #5) and then soldered the Blue LED to the stock switch that does not have the #5 prong.
Plugged everything back in and WALA all the switches work and all light up now.
So it seems there are differences on the switches and how they are made. I don't know if this will help anyone or just confused you guys more, I'm just glad I finally figured mine out and they all work!!!!