I believe the V6 4 speed automatics of 03' and 04' had 3.909, everything else has 3.727.
Under "differentials":
Toyota 4Runner History 2005
You are correct sir, I just looked around and found this by superman----->
I really don't know how much additional I can add to the conversation but I'll try and clarify a few things.
First there is actually a 4th gen with a different gear ratio than 3.73. The 03 & 04 V6 models actually came with a 4 speed A340 transmissision and not the 5 speed A750 transmission that was was geared with a 3.91 final drive ratio. That also happens to be the final drive ratio for 6sp MT FJC's as well.
When I calculated 4.10-4.11 gear ratio for 33's it was specifically to get back to factory settings (corrected speedometer), not purpose oriented like towing or rock crawling.
From what I've read on these forums, it seems that 33's and up have a much more drastic effect on V6's than they do on V8's. I've not had any issues with my V8 and factory gears. Having driven multiple 2UZ powered vehicles as well as many 1GR powered vehicles, I believe it. I'm not interested in starting a V8 vs V6 debate, it's just what I've experienced. If I had a V6, I'd probably be looking to re-gear. If your truck is hunting for gears while doing normal driving, a re-gear will solve that. Actually from everything the OP says, a re-gear is exactly what you need. 4.56's should be plenty sufficient for what you're looking for, since the results of doing anything less (even if you could find the R&P sets) would be minuscule.
For you V6's (selectable 4WD) guys, you could probably get away without re-gearing the front at the same time if you never used 4WD... If you had to. I wouldn't recommend it.
Only "drive-ability" issues that I can see is that the speedometer/odometer/trip computer etc. will be a little off. If you have a means to re-calibrate for tire size and gear ratio, then by all means, you should do it. But I don't see anything that would be detrimental.