Here's what I've found
It looks like a few ppl have stopped in to read this thread so I figured I'd post a followup. I called Softopper yesterday along with Killer Toy Tops. Here's what I found, hope it's helpful for those thinking about a purchase.
With Softopper I spoke with Bob, and asked some specific questions. I asked the thickness of the material. He said he wasn't sure of the exact measurement but that it was the same thickness of the Wrangler tops. Not being familiar with those, I assume it's fine. I've asked him how long they've been making the tops for the runners. He said it's been about two years. Searching through the site I didn't see the ability to buy just the canopy. He said that you'd be able to, but that they haven't had anybody request that as of yet. As of yesterday (20100428) they were in stock and ready to ship. The stetup for the runner also comes with the bag so that when you fold it down over the tailgate it will be tight.
When I called KTT, I spoke with Sean (sp?). Awesome guy, full of a LOT of Toyota knowledge. (Ended up talking with him for a while about turbo runners and how they differed from the turbo trucks.) This was something he started out doing as a project for himself a few years ago, and wanted to try to make a few for others. I again asked about the thickness of the material used for the canopy. He said he wasn't sure but that it wasn't vinyl, it was thinner. I believe there is a link on the site to the company that provides the material. They should have more info. I then asked if the top folded down. This was an advantage that I was looking for. He said that was one of his original designs but he didn't like it. Said that when it folded down it would prohibit the tailgate from opening. So if you are doing a lot of loading/unloading of gear out on the trails it would get annoying fast. I believe he said that when the Softoppers are folded down they need to attach to the gate. (I may have misunderstood that part.) In order to take down the rails, you'll have to use the quick release and then store them somewhere in side the runner. He did say that you could ride with the canopy off, and the turbulence wouldn't effect these structures. Talking some more, I asked if he has any in stock and if they were ready to ship. He said he does each top to custom orders. Said everything he's gotten in has been different. Right now the wait was a couple months. I didn't ask about a warrantee.
After hanging up and thinking some more, I decided to go with the Softopper. Putting money aside there are a few main reasons I went this way. First, I don't see myself loading things in and out of the bed that often. Second, I like having the ability to roll the sides up and down without having to completely remove them and find someplace to store them like you'd have to on the KTT. You can see that from the pics on the site. Next is I like the ability to quickly get the top up and down. Having a truck and living in a city, I've often found people's empty bottles, half eaten muffins, etc. left in the bed. I'd like to try to avoid that in the future. Finally, Time. Hoping the warm weather finds us in the NE soon. Walking out to frost on the runner yesterday morning wasn't the best of ways to wake up at the end of April, but thinking it will get its use very soon. I went ahead and ordered the setup yesterday, and received an email with a tracking number saying it was shipped a few hours later.
I'll post pics opinions when I get it next week.
