Congrats. The JK's do ride like Cadillacs compared to most previous Jeeps of any type, lifted or not. Those who do not appreciate this fact ought to try one out!
When it comes time to put a new suspension under it, I can say the AEV suspensions ride better than oem and improve handling, which is a feat.
There are more than a handful of roof rack options from body mounted racks to body and frame mounted racks to top mounted racks.
For top mounted racks take a look at the soo to be released AEV 3/4 length rack, the Front Runner 3/4 and full length racks and MBPR racks which give different choices for length. I believe the AEV rack will tie into the roll cage for additional support, but I'm not sure and awaiting its release for details. Front Runner has a RTT QD mounting system which is pretty inovative and attractive to me because of the ability to easily mount/remove the RTT.
For body and/or frame mounted racks take a look at Garvin Industries Safiri Rack, Wild Boar, Gobi.
Here is a photo of the soon to be released AEV rack, which is my favorite, especially if it does tie into the roll cage:
I have a small roof mounted Garvin Industries rack, which would just accomodate cross bars for a RTT, and it is well mounted with aluminum backing plates on the inside of the roof, but it is a little too short and a little narrow, imo. Here's a photo where you can see how long it is, it would rate as a 1/2 rack, imo.
Links:
Front Runner (lots of cool gear here!):
http://www.frontrunneroutfitters.com/expedition-central-page5
Gobi:
http://www.gobiracks.com/
Garvin Industries:
http://wildernessracks.com/
MBPR:
http://mbrp.com/
AEV (nothing on the rack yet):
http://www.aev-conversions.com/
Wild Boar:
http://www.wildboarproducts.com/
Hope this helps,
JPK