The Tundra's corrugated bed made things a bit challenging.  Since the header beam at the front of the bed - to which each main support beam would be fastened - would be running across (and hence, sitting on top of) the raised portions of the bed, the header was going to sit higher than the beams which, for stability purposes, were going to run lengthwise in the grooves.  This caused the main beams to sit about 1/2" lower than the header.

To raise the beams 1/2" to make them flush with the header, I purchased some pre-cut strips of wood at Home Depot and fastened them to the bottom of the beams.  These were 2" wide by 1/2" high.  Luckily, the grooves in the Tundra's bed are also 2" wide, and the strips fit perfectly into the grooves. I found these in the section of Home Depot where they  have premium, cut pieces of poplar and oak.  Later, I found a cheaper solution in the area where they have molding; they also had many more options in widths and thicknesses there.

One of the 1x10s with the 'riser' installed. 

After attaching the risers, I installed  the 1x10 header which runs parallel to the back of the cab, and rolled up some extra pieces of carpet to fit between the header and the front of the truck bed. If the base does move, the carpet will provide a bit of a cushion.  I didn't want the header up against the bed in order to prevent vibration noises.

I did decide to add some more support to the base after this mock up.  I don't have pictures at this stage - you can see some further on - but I added several cross-beams for structural support, and also to provide an edge against which the hinged doors will eventually rest when closed.

With everything mocked up and fitting well, it was time to take it all out and go get the cab. 

I way over-researched this part.  I spent days at the computer checking out various manufacturers and models; made repeated trips to numerous showrooms....

I ended up getting an A.R.E. MX topper.  It's about 6" taller than a standard topper, which provides the extra headroom to allow sitting up in the back.  This will be a big plus in general, but especially if we need to hideout during bad weather. 

The MX has a fold-down front sliding window which will allow for access to the back of the truck (the back window of the Tundra goes down all the way).  The MX also has sliding screened windows on each side, which should allow for good ventilation.  I was tempted to go with a better looking model, but function won out over form, and I think this looks pretty good anyway!