I primered and painted the frames and finally got them reassembled. The vent windows will not stay in one position so I'll put some rubber pieces in the holes of the brackets to take away some gap. This should give them more pressure to keep them more stable instead of flapping around in the wind.
Assembly was pretty much a breeze.
Start with the non sliding window. Prop up the frame just like you did when removing the glass. You can put the window in toward the back of the frame instead of starting at the very front. You have to separate the frame a little and work the glass w/weatherstrip into it's place. The weatherstrip will tend to move, so I used baby powder to help it all slide into place.
After the non sliding window was installed, I put the rubber stop in. That's the piece of rubber that goes to the back of the frame. It is a stop for the sliding window.

From this point on, until you screw the frame together, you will need to make sure the glass does not come out of the frame.
Next is the new window channel felt. If you can't get the felt in one piece, try to make the splice at the top of the frame. Install the felt in the bottom of the frame, starting at the end of the stop, but don't go past the seam towards the latch. Leave the rest going straight out the front of the frame. This will allow you to prop up the back of the frame so you can slide in the window. Just like removing the glass earlier except the felt is not removed. Once the glass is all the way to the stop, put the seams together and secure it with the bar and screws. Finish putting in the felt all the way to the back until it touches the stop and trim off any excess.
Slide the window back and forth and check to see if it latches easily. If it slides good, install the sash. Once the 2 screws holding the sash in are tight, check the sliding window again. If the window slides good, slide it all the way open and install the vent windows.