I've towed track cars with my two 4Runners for a total of 35K miles or so. Here are my suggestions:
Don't just put the shift lever in "D", engage cruise and expect the truck to do all the work. Learn what gear you're going to need for any given situation and manually downshift the transmission before the vehicle takes up the load (for example, at the bottom of a hill that you're going to climb). Make things easier on your 'Runner by easing up a bit when climbing hills; this will help the 'Runner stay in a higher gear and keep the rpms lower.
Cruise control has a limited IQ, and will keep the truck at whatever speed you set, calling for more and more power to do so until the truck is in whatever lower gear is necessary. If you shut off cruise and allow the truck to gradually lose speed as you climb a grade, you'll find that losing as little as 5 - 10 mph will let you climb grades in higher gears than you'd need with cruise engaged. That said, as long as the rpms aren't in the red zone, you're OK for a few minutes at a time.
Towing in 5th gear ("D") is fine, as long as the truck will manage it without unlocking its torque converter. When the torque converter is unlocked, its two elements churn, building up heat which will shorten the life of the transmission. Learn to watch the tach: If you see the rpm jump 2-300 rpm when speed is steady, it means the torque converter has unlocked to provide a little more torque to the drive wheels. Occasional brief periods of this are OK, but if the converter stays unlocked for more than a minute at a time or repeatedly unlocks, it's wise to shift to 4th gear and stay there. Toyota does recommend towing in "4".
Our '03 V8 'Runner currently tows a 5500# enclosed trailer with 55 sq ft of frontal area. It can't manage this in 5th gear ("D") unless the terrain is flat and there's no headwind. So most of my towing these days is done in "4" (4th gear), which means 10 - 11 mpg!!!
If you're towing 2,000 #, be sure you have trailer brakes. Toyota recommends trailer brakes for trailers weighing 1,000# or more, and most state laws require trailer brakes for trailers weighing that much. If your trailer has electric brakes, you'll need to install a brake controller for them to work. If the trailer has surge brakes, no controller is needed. Learn to manually shift to a lower gear when descending grades so the engine and transmission can help you brake. The rule of thumb is to use the gear which will let you maintain a steady downhill speed without using the brakes to do so.
Good luck. Your V6 'Runner should do a fine job towing your ATV, if you learn a few skills and give it a little help. Please holler if I can be of more help. (
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