An absolutely great truck rack system for you would be to put the
Yakima Q Tower Half Pack on the Toyota Tacoma cab roof. It includes two Q16 Clips (these are made for the 200 Toyota Tacoma), two upright Q Towers and a single cross bar. This will be the front cross bar that you will connect the kayak carriers to. Get the 58 inch cross bar as this is the length necessary to carry 2 kayaks. Then get the
Yakima Outdoorsman 300 (compact size) truck bed rack half set system for your truck bed. The Outdoorsman Towers comes as a half set allowing you to use in combination with the Q Tower half pack. You will also need to purchase one 58 inch cross bar to use with the Outdoorsman Towers. You can then connect the the other half of the kayak carriers directly to this cross bar. The Towers quickly clamp onto the bed siderails and will not impact your tool box.