All I've been researching for the 4.0 is the air intake, since my donor 4.0 doesn't have one and there's no way I'm using the 'intake' on the 4.2.
There are quite a few different air induction systems for the 4.0. Since it's fuel injected, nearly every company has something that'll bolt on to the 4.0. Quadratec has quite a few of these in the catalog (and surely online too). Here are a few Q-tec part numbers...
AEM Brute Force Cold Air Intake Kit - 244.99 p/t 17012.003 - claims 13 hp and 15 ft/lb
Funnel Ram Intake System - 169.99 p/t 17006.002
Hesco High Flow Throttle Body - 439.99 p/t 17009.103
1989 Jeep Wrangler - 4.0 swap, 32" BFG M/Ts, RC lift
1997 Acura 2.2CL
2008 Honda CBR600RR Graffiti Edition