When I did this type job a few years ago I remember having a hard time finding the proper channel for the windows. I wound up using some kind of felt material and since then the windows are stiff when openning or closing. So I guess I'm saying to be sure your new channels are a comfortable fit prior to adhering them to the door frames. I'd be very interested in knowing the kind of new channel you're using and how that works out. I want to redo mine sometime and could use more specifics on materials.
The vent window rubber is a little difficult to get seated and the window is a lot stiffer for closing after install. I got some of those security type locks from IPD so I could close the window all the way. It's OK now, except for one small drip leak.
Anyway, please post your results and tips during/after your project.