If you have already checked under your carpets (someone may have spilled milk or an entire cola, etc and it's now molding) and they appear to be clear, then try spraying some Lysol down into the front vent below the windshield below the passenger windshield wiper WHILE your fan is turned on full speed and in the OPEN (not recirculate) position. Give it about a 5-10 second shot then let the fan run for awhile.
Pull your cabin filter out and give it a shot too. Worse case scenario... your truck has a pleasant anit-septic smell instead of the homeless person effect.
The Good Lord only knows what some people do to their vehicle's initeriors. I don't want to know, personally. I'm just sayin...
Scout had a "funky" smell to him for awhile, expecially in the summer heat. I kept giving him this Lysol treatment every four weeks and now it is subsiding greatly (FINALLY!).