I just went through this and thought I'd update this thread with my findings.
First, going with a Tacoma shaft IMO is the only way to go. My truck has never drove so smooth and when I had the shop look over what I had in there I was really disappointed in how it was built.
Sourcing a shaft:
Any drive shaft from an extended frame can be used. So any motor, tranny, 4x2 or 4x4 combination is fine as long as it's an extended cab or double cab. The stock shaft is a two piece job and the only difference is the front extension piece between the configurations and we don't use that.
Also, late model shafts will likely have a damaged Yoke assembly. Since the total value is high on these trucks the ones in the yards have taken one hell of a beating before getting there and the yoke is one of the failure items and a few yards sent me a shaft with out it thinking it was complete. So be sure to ask that the yoke is present if ordering on line.
At some point there was a change in the CV design.
The older design has zirks located on one of the cups for the u-joint and a right angled one inside the joint for the centering section.
I got a 2002 shaft from a 4x4 4 cylinder that the u-joint jirks are located in the center of the spider and the centering section zirk is straight out of the joint. This is a real nice setup for greasing. With the shaft rotated with all three zirks at 10:00 the joint is actually opened up for access. The attached picture shows the three zirks.
Re-working the shaft:
The shaft needs to be shortened and because of the balloon tube used in the factory setup it needs to be re-tubed as well.
The distance from flange to flange fully compressed is 31" and this leaves about an inch expanded when installed.
The shop I used spins the shafts up to 3300 RPM when balancing. My understanding is that most shops only go up to 600 RPMs. The higher the RPMs used during balancing the better the out come.
In the end I actually bought two shafts. I had gotten an older style shaft that has been modified and is the one that I'm currently running. Unsure of how things were going to turn out with the first shaft as it has 110k on it, I found the 2002 shaft during my weekly travels for 100.00 so I picked that up for a spare if needed.
This was a lot of work and took about 6 weeks to get done as the repeated yoke issue wasted some time. But with a good shaft and the right shop, you'll have what I consider the best solution for our truck short of buying a new Tacoma shaft from CDan and modding that at over 600.00 just for the shaft.