Well, a 5 speed swap is much cheaper than your reman auto trans quote. I think you could do it for $600.
$300 trans/tcase/flywheel
$100 clutch
$100 hydraulics
$100 misc parts to get it all going
$300 trans/tcase/flywheel
$100 clutch
$100 hydraulics
$100 misc parts to get it all going
don't have that kind of money I would rather stick my money in my fj40.