Got it rigged...thanks to all!
I got some Yakima racks from EBay that came off a similar truck. This set came with the bars, locks, mount towers and the "mounting feet" specific for the Tacoma 4 door. I also got a set of four mounting points/plates for the cap and the special clip bracket for these mounts for the towers. My end result is that I can mount the pair of Yak bars on the cab, on the cap or split and have one on the cap and one on cab...a range of options.
So far here is the cap setup for a VersaBoard (bout 11' as I recall). Note my Leer cap roof line is about 4" higher than the cab...a bit of headroom and keeps load over the cab very well. With the 16' canoe I will likely use just a rear bar on the Leer cap and one on the Tacoma cab.
Also...the nicest feature and why I hunted for the long bed...fits a cot for sleeping (if your under 6'). "Roll-a-cot" brand with no middle leg where wheel well is. The green container has a 12" loop of nylon web strap pop rivited to the side...allows the strap to be looped over the tiedown slider and prevent sliding around.