Finally have the rig up and running with the 5spd and everything is working great. I forgot to remove the starter relay and join the two wires together so I currently do not have blinkers, but other than that it is running great. There is so much more power compared to my other 1st gen 4runner with the 5spd. I didn't think the 3.0 was too lacking in power, but driving the same rig with the 3.4 and it feels like it has so much more power. With the 33's and 4.56 gearing I can easily get the tires to break loose at a take-off which was unheard of with the 3.0.
One thing I need to do is change the exhaust, I currently have a magnaflow and it is just too loud for my taste.