I looked at Rock Auto. Fel Pro MS94790 91-98, Fel Pro MS93094 99-01. I think on the 99 year, there were some with the old intake and 0603 head, some with the new intake and the 0603 head and others possibly with the New head 0331 and the new intake. ??? I just bought a head off a '99. It had the 0603 head.
Now, for the 2000 there are two types of exhaust. The Federal and the Cali. On the 01 its the same, and the same as the '00 Cali, ie two precats. They also use the cast iron manifolds. The Cali has a piece with the precats between the exhaust manifold/header and the down pipe. The '00 Fed, the down pipe extends up to the exhaust manifold/header.
As I know it, the 00-01 aftermarket headers have a bit smaller diameter pipe. It would work for the 0603 head, but would be a 'port match'. You want about 1/8 larger diameter pipe. I can check this tonight, as I have a 0603 head off a '99 and a BKK exhaust header for a 2000+.
I'm in the stages of two builds, and a deconstruction of a '98. Don't mention the '88 MJ, with an '03 WJ 4.0L. I do plan to put a 0603 on the '00 and a '95 head from Russ, on the '01. I will use one of the Doug Thorley 91-99 headers on them. Then adapt the down pipe to it. Then again, I might look into a 'custom' down pipe.
Edit:
https://www.bankspower.com/i-2581-e...99-jeep-wrangler-4-0l-1991-1998-cherokee.html
https://www.bankspower.com/i-788-ex...01-cherokee-and-1999-2001-grand-cherokee.html