on a 1" body lift do you need to extend the shifter linkage?
No
I put a 1" on my '89 Runner (it has the AT) and added nothing.
Probably shuould have loosened/adjusted the power steering linkage first though, the seal leaks now.
IF you use high-grade hardware and tighten it sufficiently, the "stress" really is not an issue. It's not liek you really have a lot of bending/sheering forces on it (under normal circumstances).
You do ru na chance of breakage in the event of a really hard collision, but a normal body mount can break from that too.
On a well-designed lift, the contact patch between body/frame is exactly the same, if not greater, than the OE contact... even on the normal setup, the body does not ride ON the frame.
That said - 3" lift LOOK pretty stupid.
If you are clever you can hide it pretty wide, but it takes work. E.g., nice big thick rocker panel gaurds hide the frame hanging down below belly, move bumpers, add plastic covers aroudn all the wheel wells, etc etc.
Just not a fan of them though.
If it's just for clearance - sawzall the fenders - good chance to cut out the famous Toyota rust anyway!