the K&N on 01-03 4.0's are mounted to the engine..alternator bolt to be specific...and there's gobs of room underneeth the filter stock, so 3" raise shouldn't be an issue. If an adjustment of the angle of the k&N tube needs to be made, no biggie. loosen up the clamps at hte throttle body and turn it a little.
The MAC intake set up for 01-03 4.0L's are mounted to the body....so some modding will need to be done(i still gotta mount the damn thing lol). the intake mounts to the old lower rubber grommet hole things that the stock box attached to.
Thunderbolt works perfectly fine w/ a bodylift; you're using the stock intake tube, so it flexes really easy.
So get out there....and do it!
'01 XLT disguised as a '03 Fx4 Level II
Big. Loud. Slow. Bright.