I use the Thule gutter foot system withe the Malone J-loader racks that hold the yak upright., it's no drilling at all. The Thule system tightens down onto the drip edge of the freedom top and secures that way. You can't take the freedom top off and still use the drip edge method of securing racks, it just won't work because the drip edge is part of the hard top not the door or frame of the Jeep.
You may want to look into the gobi racks that mount around the outside of the Jeep and are just above the hardtop. Personally I'm not a fan of the look and they are usually pretty expensive.
You may be able to get away with taking the T-tops out of the freedom top, that will leave the back portion of the hardtop and still allow for a "gutter" drip edge style rack to run across but depending on the length of the kayak that my not be a ideal purchase point of securing.
Heres mine
![20150312_175132.jpg]()
