My truck is a 1986, so I'm not sure how much of this will carry over. But I was in a similar situation as you were, so I hope at least some of it will translate to the second generation Rangers or give you some ideas:
When I first got my truck, it had been sitting (according to the seller) for five years under a tree--last time it was registered was '06, so take it with a grain of salt. Only noticed a terrible odor of rat poop and urine once we got it home. Further inspection revealed the rats had decimated the jute behind the driver's kick panel, built a nest in the vents, and pooped all over in there.
This is how I went about cleaning it out:
I first closed all the vents in the cab and turned the fan on high, spraying Lysol into the cowl. I emptied the ~0.5 full can over a course of two hours while occasionally switching between the routes to ensure full coverage of the system. This sat for a few days before I removed the fan and used a borescope to locate all debris in the vents. A bare shopvac hose was able to get most of the way inside (about to behind the dash warning lights). The dash pad was removed at this point (huge PITA) which enabled access to the remaining areas up there.
I finished up by mixing some Bissell pet odor eliminator and manually wiping down the vents as well as I could. The truck was left undisturbed for about a week with the windows cracked. This was done 2.5 years ago, been through sustained 80-90 degree summer weather, and the smell has never returned once. The occasional passengers, when prompted, confirm that there's no indication any organic waste was ever there.
A few notes: do not neglect the heater core housing. A rat skeleton was found in a nest there; did the usual Lysol and Bissell treatment to the inside of the enclosure while the core itself was treated with foaming A/C coil cleaner from Lowe's. Additionally, when the core is removed, it enables decent access to the lower vents. Don't forget to wipe down the fan, too. 36 years of dirt (in my case), regardless of infestation status, has a tendency to smell.
All this being said, everything was accomplished while both the seat and carpet were removed. Yes, it would be doable with the seat in, but it'll definitely be a much worse endeavor that way.
Hope this can help.