I have access to a pair of axles out of a 64 FJ40. Will these work under a sami? I plan on going with shaffer's coil kit front and rear if that matters.

Yes they will .I ran a rear and was planning front swap when i swapped vehicles:)It was a easy swap.

thats the set-up I will be running, my sami is up on jack stands and my LC axles are rebuilt. Just waiting for my Shaffer kit to be delivered, its being custom made for the LC axles. Its gonna be sweet!

You will have your work cut out for you with this one. I did a pair of 67 FJ40 axles, and swapped disk brakes to all corners. If you plan the disks, you will need to order new side gears for the front axles, and new inner axle shafts. Mini truck knuckles and outward gear fit right on, but you will have problems with the bushing that holds the outer end of the inner shaft. I had to press mine out, then have them machined for the shafts to fit. Other than that, easiest swap I have performed.

if you go w/ cruiser axles, try to find some from '69 and newer to convert to disks...pre '68 has course splined axle shafts and dont use birfield joints (ball joints=shitty) and you can not convert them to discs unless you get the fine spline 3rd member and shafts and birfields...if you get some w/ the fine spline (30 spline) inner shafts and birfields, the mini truck parts bolt right on pretty much and you get stronger birfields while your at it!...