Patrick, can you take some close up photos?
It appears the top front of the glass is too high.
1) It should be level with the vent window frame.
2) It appears to have pushed though the top corner rubber tip (which should be flush with the top of the vent frame, which yours is). The rubber tip has a rubber top, glass should be adjusted to meet that top, not bow it up or push though it.
The front nylon guide doesn't appear to be in the channel track at the top. If that's true, it's tilting the rear of the glass down.
I think once you get the nylon guide in the track and the front glass is at the correct height, that may help correct the current angle (rear too low, front too high).
"It is the rear curved area on the door glass that is sticking out about a half inch. The weatherstripping seal is good fit until getting near the “sticking out” curved area of the glass."
Does "sticking out" mean the glass is 1/2" out away from the rubber seal?
Or is the glass 1/2" away from the top curve of the hardtop?
Can you take some close up photos of that? Example, rear edge of the glass looking forward.
"The window channel has some tight areas in it and I’m going to have to adjust the opening of the channel to allow the window to slide without binding."
Confirm both the front and rear tracks allow the glass with the guide on it will travel up/down by hand. You can do that by removing the front track with the glass in it and trying sliding it in the track while it's outside the door. Then pull the glass out of the front track and slide the glass in the rear track that's still in the car. If that works, the tracks should be OK.
The tracks maybe out of alignment.
The front and rear channels are curved the same as the glass. If the channels positions aren't mirrored, the glass will bind somewhere in the tracks. Example, if the rear channel is set with the top all the way to the inside of the door and the bottom is to the outside that angles the glass to the interior. If the front channel is reversed; top to the outside, bottom to the inside, the glass will angle to the outside. When trying to roll the glass up, it will bind somewhere because the tracks are not mirrored.