they all had the 5spd actually.

Lexus GX470

i second the stay away from the factory nav system. its integrated into the HVAC system. so if you ever do want to upgrade the stereo you lose the ability to control the temp of AC or defrost ect. plus the Mark Levenson sound system is nothing special other than running on a special OHMs thats not supported by most aftermarket speakers -basically all of this means that if you have Nav you are stuck with it, and if anything ever fails or goes bad its paying lexus dealer prices for new stuff.

some of the GXs had the 3rd row seating, its nice, mine does and i like it, just used it yesterday taking the wife and parents and kids to the beach. they are basically a V8 4th gen 4runner like @IanB said. its on the 120 chassis so all most all 4th gen 4runner suspension or lifts/skid, etc. can be used -also some FJC stuff as well.

i have a 04 with 137k mi, no timing belt yet -yes i know i need to get hot on that soon, but it runs great and has been a joy to own and drive. i am very happy with it!