1. No manual transmissions for the 4th gen. 2003-04 V6s have a 4 speed, 2005-09 V6s have a 5 speed. All V8s have a 5 speed.
2. Both engines are just as good. The V8 have been around longer, since 1998 and it's a bulletproof engine.
3. As mentioned, 2003-04 V6 have the 4 speed transmission and 2005-09 V6 have 5 speeds. The 2003-04 V8 were non VVT-i and the 2005-09 V8 has VVT-i giving it a bump in HP and torque. In 2006, the 4Runner got a face lift, adding projector headlights, LED taillights, different bumpers, cladding and flares.
4. E-locker is only on the 2009 Trail Edition 4Runner, it's a 4WD SR5 V6 with different goodies.
5. I personally would look for a 2008 or 2009, because VSC off was added from the factory. Side and curtain airbags were also made standard for the 2008 MY. I like creature comforts, so naturally, I would look at a Limited.