I drilled a yakima rack into the side of my hard top. I'd done my pick-up truck shell before, and the Jeep top was far easier. If you decide to do side mounts instead of rails, let me know and I can tell you what you would need to get.
I keep the rack off most of the time, and when I need it I throw it on. Takes about a minute to put it on. I've run bike mounts and a Thule rocket box on it with no issues.

This was the only pic I had. Not the best one of the rack, but it does the trick.

 

I drilled the roof too, to carry snowboards, so far so good, no leak and nothing broken..

 

No problem...I'll let you know when I get the tracks in. Good luck with the adoption!

 

I did not want to drill at all. I bought Thule racks that go into the gutters of the top. It works very well and no holes! I would reccomend if you don't want to have holes, and plan to take it on and off alot (like for one season at a time).

 

The only problem I see with that option is that there isn't much of a raingutter track to work with. It doesn't seem like it's long enough to be able to place the Mega Warrior on top.

 

I would not put much load on that top anyway. It is not exactly load bearing material. The rain gutters are good for however much I use it for, which is snowboards. The Thule rack is good for up to about 150 lbs. I wouldn't put much more on that top anyway.

 

I put the Thule tracks on my hardtop. For a little added strength, I filled the double walled channel, at the edge beneath the track, with Great Stuff foam.
It's very sturdy.
I've carried a "clam shell" car topper loaded with luggage, etc, with no problems.
DB888 did a write-up showing the install...

 

How did you manage to fill it with Great Stuff? Did you fill it when you drilled the holes? I think this is the option I'm gonna go with.

 

I've never cared for drilling holes in the roof much, so I'd recommend purchasing a safari rack that allows you to tilt out of the way.
Like this:
http://www.quadratec.com/products/12041_004_07.htm
It's kinda pricey, but the best gear always is pricey.

 

Here's what I did.

Didn't want to drill holes. So far has been strong enough for my canoe at 60+ mph down the road.

Blue Mesa

https://www.jk-forum.com/forums/show...ight=Blue+Mesa