Just to have the (IIRC) correct info out there: the interior (dash, wheel, etc) of the pathy was redesigned along with the facelift in 1999.5. The center consoles are the same from 1999.5 to 2004. The only differences being on options like auto/manual, 4x2/4x4, heated seats etc.
That said however, if you don't like it, I think a flat piece of aluminum would be a good place to start, and you could build it so it surrounds the shifter, and then "steps up" into a cupholder and then armrest. Kinda like this: http://www.4wd.com/Jeep-Interior-Parts-Accessories/Subwoofer-Security-Console.aspx?t_c=9&t_s=411&t_pt=8379&t_pn=TFY066-03
You may be able to take some measurements and retrofit it in, or copy the design. Just some ideas