Tape comes in different thicknesses. I used urethane window sealant instead. The advantage is no water leaks in. You set the spacing of the window with some small pieces of tape to center it. Mask the window and the channel. Then squeeze in the urethane, wipe off the excess, remove the tape and let it set overnight. Flip it over the next day and repeat. Don't set the glass in a full bed or you will never get it out if you need to.
excuse my ignorance but i'm confused. Are you setting the glass out of the door? And if so how are you getting the lower channel to mount to the regulator? The lower chanell is inside the door, what are you sealing from water getting in?