Four sea kayaks. Are they plastic or do you need to treat them gingerly? Plastic, no problem--heave em up there on top of each other if need be. If they are yaks that want to be babied, you probably need to carry them on their sides, because four across is going to span 7-8 feet, perhaps too wide for your truck.
And a storage shelf...what exactly is that?
And be able to carry bikes, a challenge, if this storage rack is in the bed.
I have a Tacoma. I wanted to put a rack on the roof and a rack at the midpoint of the bed so I could carry boats centered on the truck. But Yakima changed their tower and clip arrangements such that they did not sell clips for my truck that could be mated with my older towers. This ticked me off, and I ended up slapping together a 2x4 rack as a temporary solution. That was January, 2002. I've replaced the truck and moved the temporary racks into the new truck. My racks cost me less than $50 to build. They are not perfect.
One disadvantage of my racks is that if I want to use the truck to haul stuff, I usually need to take the racks out. It slides in and out in under ten minutes, but still, ideally, I could just leave them on.
I retrofitted the racks with one pair of drop down wheels, so that I can move the rack and only have to hold one end of the rack. All four uprights are mounted to a rectangular base of 2x4s that lies in the bed, so I need to move it all at once. A nice feature is that I can leave boats tied on the rack and slide the rack out with the boats on. Often thought that if I were to do it again I would build a storage box into the base so that I could keep paddles, pfd and all that gear in the rack/box, and move it all at once. Of course, that make it so heavy that it would be harder to move.
I'm thinking about getting some of the racks that mount on the side walls of the bed and that don't interfere with sliding materials in and out of the bed like my current rack does. I know Yakima sells 'em, I think Thule may, and there are similar products available from other makers. These aren't cheap. They have a pro in that you can buy accessories to adapt the bars to different kinds of gear, but the accessories are not cheap either. I think you'd be in the $500 neighborhood to get a pair of these side-wall-mounting towers and bars. I like that you can drop them down when not in use to lower wind resistance. A con is that if you hit anything (e.g. overhanging tree) with these towers, they crumple the side-wall of the truck bed...seen that on two trucks. I have hit similar (a fence) with mine, and it cracked the 2x4 upright, which I replaced for a few dollars, so that is a plus for the home-made solution.
Well, long and rambling here. If you think you are building, let me know and I will send you pictures. But that is a tough challenge.
Good luck with it.