I was pricing roof racks for my hard top and discovered something. If they were made of gold, they would be cheaper, because they must be made out of unobtanium.
New Yakima racks are over $300 new, and not much better on craigslist. In fact finding a decent roof rack at all on the cheap is not easy so I looked for an alternative.
My wife has a 95 Grand Cherokee with a factory roof rack. I looked at that and figured it would work good. So I found one on craigslist for $40.
I got it and having previously measuring the length of it, I cut 14 inches from the front end of each rail. The angled end caps slide off and you have to trim the rubber base as well. An air powered cut off wheel worked perfect for this.
The factory torx screws that came with the rack are not long enough to go through the fiberglass hard top, so I went down to the hardware store and bought 10 1/4 x 1" stainless steel allen drive button head screws, 20 1/4 lockwashers, 10 1/4 nuts, and 10 1/4 x 1" flat washers. I also bought a role of putty tape, found in the plumbing section.
I measured and squared up the rack on top of the jeep and drilled 10 1/4" holes. Then I lay down a 5 foot length of putty tape for each rail (The RV industry uses this same exact stuff for sealing in anything bolted or screwed to the exterior rv walls and works great). I then put a lockwasher on each screw and pushed it through the drilled holes. I then put a short piece of putty tape on the back side of each flat washer, then another lock washer and finally the nut. As you tighten each nut it will press the putty into any gaps and also squeeze out from under the washers and the rails, for a great water proof seal.
It was extremely easy, and now all I have to do is find a good cargo basket..... or make one.
Hope this gives you an idea for your rig.