I've found a replacement glass run for the factory slider windows, and it's a Ford part!

It comes from the sliding side windows of an Aerostar. After cutting the one outer lip off, it's 3/8"W x 5/8"H, so it's recessed in the channel ~1/8".
The top L pic is the unmodified run in the channel, but it doesn't touch the bottom because of the extra lip. Top R is after cutting the lip off & pushing the run all the way down. Lower L is with the glass in place. Lower R is the uncut section compared to the cut section.