I feel your pain brother.... I had to bite the bullet and get a LEER cap for mine too. I bought a brand new tonneau, but it proved to be too impractical. My kids say it looks like an old mans truck now..but what the heck, at 47 I AM AN OLD MAN! I'm thinking a couple of inches of lift will help it look better. Oh and BTW, if your truck hasnt bottomed out because of the SUCKY suspension of an '06, it will once you get the cap. It's not too bad, just certain speed bump-like humps will get ya.
Do yourself a favor and but a Toyota rubber bed mat too, otherwise everything slids around!
I tow with a trailer, screw luggin that stuff up a ramp, the tailgate can't take it anyway!