Hey there Mark - I saw this thread on the forum and showed it to my wife without saying anything. She glanced at it and said "oh good, you finally got around to posting the questions you were wondering about"!
We also have a 2007 309 and have the exact same issues. We've had it for almost 6 years and the flooring problem has only recently started. So don't know if it's just been a timing thing (like the original adhesive has been slowly breaking down). Or if we had a particularly hot summer this year or something. I was going to try some differing adhesives, but haven't gotten around to it yet. When I do, I'll probably give Rick's suggestion of contact cement (above post a try). Let me know if you are successful with anything. And when I get around to it, I'll let you know any success I have.
Regarding the splotchy stains, we have the exact same. And I concur that they do NOT seem to be associated with water staining or leakage. I wonder if they could be some kind of mold or something from the back-side. I figured the only solution was going to be to eventually paint, but haven't gotten that close to the top of my to-do list yet.
Anyway, this post doesn't offer anything in the way of help, but know that you aren't the only one with the problems!
Dave - Port Charlotte, FL