I know what you're talking about, on the pickup the filler door is right above the fender flare, where on teh 4runner it is about 6" forward.
If you want, weld it shut, and get a 4runner door and pocket (looks better IMO) or you can just get a hose that has an "S" bend in it, to make up for the difference, and place it inline of the filler neck.

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