For future reference... in the taco world, for OEM CV shafts, there were two types, we called them:
The green label shafts (ADD hubs):
and the blue label shafts (Manual hubs).
(Best pic I could find, bottom shaft)
On the the two 4runners I've owned (96 and 00), and the others I've worked on, they all came with CV shafts that had no labels on them. What I did notice about the ADD Tacoma shafts vs the ADD 4Runner shafts, is that the Tacoma shaft was straight all the way across (see top pic for reference), and the 4Runner shaft was necked down in the middle. See above shaft in the below pic for reference....
I have no idea if one is stronger than the other, what I do know is that they are interchangeable between platforms, I currently run green label Taco shafts in my 4Runner.
I also know that the rebuild kits from Toyota are completely different part numbers....
*4runner is 04438-35060 price is $43.80 from Camelback Toyota
*Tacoma is 04438-04021 price is $35.02 from Camelback Toyota
My guess is the boot kits are not interchangeable, but I've never actually tried it so I can't be 100%.
Hopefully some of this helps.