Pretty sure the problem is the downpipe(s). On our 2000, we have 2 pipes coming off the exhaust manifold - going into those 2 pre-cats. Pretty sure in 1999, it was a "6 to 1" collector - where all 6 pipes come together off of the exhaust manifold. But maybe not. Can't remember exactly.
In wranglers, I think the headpipe travels in a different direction....but not 100% sure.
Banks and JBA are the only ones I know of that make a header for the 2000. Sorry I couldn't give you definite answers...the info on this subject is limited!
The JBA one is cool, b/c you can get it coated. Its just $$$!!!
http://www.rjroffroad.com/jba-cat4ward-headers-for-00-06-jeep-wrangler-cherokee-40l-offroad-c-439-p-1-pr-17014.html
I still haven't decided which ones I like better! I dont know of anyone running the JBA ones.
http://www.bankspower.com/products/show/221/54
(picture is actually of the one for 91-95 wrangler + headpipe - wish Banks would get off their asses and take other pictures!)