URD offers a y-pipe, which removes the 2 rear cat's (still leaves the front one) and a 3" stainless exhaust.
They also have a computer tuner that you can get 15hp+ with (thought you need a wideband to tune)....
check www.customtacos.com for 4.0 mod's... lots of xrunner owners there.

89 4Runner
3" BL, M/T locks, 33"bfg mt, bilstein, Kayline, tubebumper, toyotafiberglass panels
TBI: Elocker,3.4 w/ORS,b+b,S2Sstg2cams,arias pistons,P+P intake,TRDs/c,URDpullies+7th,downey headers,MAPECU2,WEGO WB, SupraMAF,walboro255,stg4clutch, EPaOo2 sim