If you have an auto transmission, the factory 4.88's are the right gear for 31's, but might cause your mpg's to suffer w/a 5spd and 31's on the highway. Here is an
auto calculator page. Using the "Find Your RPM" calculator, plug in your current gears and tire size to get your rpm's at speed X and then try the 4.88's. If the rpms are only a few 100 higher it would probably be worth it to run them with the heavier Runner. I know a few people who like to run 5.29's w/33's in their runners w/a 4cyl. I would check the gearing yourself, just to make sure the 3rds weren't swapped out before you bought the parts truck.
As to value, if you have the 3rd members and front IFS section, maybe $400 for the set. The strength of the factory 4.88's isn't any different than that of the 4.10's or the 4.30's you have now, shouldn't have any issue Lincoln-Locking the rear.