I glued my vertical sections in place, I didn't fully trust the clips (with the toothed tabs) to hold things in place.

Although it wouldn't come into play unless the windows were fully down, I don't think cheating on material would be beneficial in the long run. Bummer they didn't send you enough to work with.

Re: junction rubber, I didn't mess with mine (out of laziness). Is it a crimped/ friction fit or is there hardware holding everything in place? I'd guess the glass would be ok unless you really gorilla'd it around.

Not that you asked, but I used a bolt cutter to trim my channel cleanly.