The gear sticks on my Rodeo were noticably shorter. So I used an extension on the transfer shifter but I prefer the shorter gear shifter so I left it alone.
I needed to remove the body attachment point of the clutch hose to hard line. I needed to make the flexible line longer but since it sort of went to the firewall and back out all it needed was a longer bracket that took the bend out of it if you know what I am trying to say.
There are two brackets which don't actually bolt the cab to the chassis but the chassis bracket loops through the body bracket (one either side) so I imagine if all the body bolts came off it would stop the body flying off the chassis (in theory). I didn't bolt them back on as I would have had to fabricate some brackets with bigger loops. I actually refitted them for the DoT inspection but removed them when I got home as their clearance was greatly reduced and they creaked around corners which was very annoying.
Everything else was fine. However on a 50mm lift people have had to remove some metal from the body where the low range shifter pulls back into low. Otherwise it hits and will jump out of low range when you least expect it. Mine just misses.