An old trick we used on junker vehicles we were tinkering with was to slice two apples in half and leave them peel-down on the floorboard for a day. It did wonders, even with an old 1984 fifteen-passenger van that sat for five years piled up with spare parts.
You could also pull the carpet and pressure wash it at the car wash- chances are it has bacteria and such that has been feeding on random crap that's spilled in it over the last few years and that's what you're smelling. Pressure wash it thoroughly then lay it in the sun to dry 100% before you put it back in.
Other than those options, Febreeze the tar out of it.
Mine: 2012 JKU Sport, Deep Cherry, Auto, 3.73s, Rock Krawler 3.5" Flex, chitty Procomp shocks, JKS Discos, Rubi rails, A.C.E. sliders, EVO ProTek Skids, EVO Rockstars, JCR Dagger with lights and tire carrier, PSC Brawler Lite with custom stinger and grill hoop, ENGO 10k with synthetic, 35x12.50-15 BFG KM2s, MOPAR flat flares.
Wife's: 2004 TJ Sport, 4.0/Auto, 2" BB, stock JKU shocks, JKS front LCAs, 31x10.50-15 BFG ATs.