I wanted to share my roof rack install on my 2005 Tacoma with Leer cap (180 something, mid-high shell).
Started with Yakima tracks, kit # 8001135
Drill through roof, install with tons of silicone sealant (already stayed dry inside through two days of rain). Take care to mount outboard as far as possible to miss the honeycombed center section if you have one. Stock the kit contains hardware for six thru-screws (10-32) per side, this could be increased to 9 with extra parts from Yakima (I plan to do this down the road for good measure - PN 8810155 $10). Each of the 12 inside mounts is a 1.5" round plastic hemisphere with steel threaded insert. These are actually handy for mounting hardware to the inside roof - for instance I'm going to hang a webbing 'shelf' for skis up there.
Megawarrior basket rack with extension kit (pretty ordinary, though I replaced the hardware with stainless screws and used nylock nuts and loctite)
Yakima expects you to buy tower kits and crossbars. Then, your roof basket ends up 4" elevated off the roof and puts more torque on the tracks. I found the tracks are just the right size for 3/8-16 carriage bolts (some were tight and had to be wiggled into place with pliers). The Megawarrior brackets are made for a very sloppy fit with 1/4-20 hardware. So I overdrilled for a tight fit for 3/8. The plastic lower bracket is easy. The steel upper bracket requires a drill press. Then the rack mounts directly to the tracks. I used nylocks and lock washers and 80 ft-lbs just for peace of mind.
The rack sits only 1" above the shell for less shear load, less frontal area and air drag. There is about 3/8" deflection with my 185 lbs bouncing dead center as far from the supports as possible. That said, I plan to add a third bracket kit in the middle as soon as I can get the parts from Yakima (PN 8870040), just for overkill. Likewise, the intended mounting has "ears" on the brackets to capture the main spars of the Megawarrior and prevent the rack shifting side-to-side. Once I tightened down the brackets, I could not get the rack to move with any amount of shoving. But this afternoon I'm making some swaged cables to connect each bracket to the nearby spar to prevent shifting (unless someone has a simpler idea?)