Did you try the full adjustment in the service manual? It has those guides adjusted when the glass is an inch from the bottom with the 3 track screws and the 3 glass attaching nuts loose. Then tighten everything down starting with the nuts on the glass once it's up and sealed properly on the top and rear edge (pry up and rearward on glass).

I've only gone through the adjustment after having the glass out but I have seen before where it can bind when it's not adjusted right.. 3 of my Plymouth windows bind up bad so I guess i'll figure out soon enough what works best on those.