It took me awhile to finally get the input shaft to finally slide in.....
Just my thinking... trying to get my engine, dangling from a cherry picker, to drop into my engine bay and sit down on the motor mounts and the frame rails was difficult for me, I probably spent 1 hour man-handling it before I finally figured out the combination.
I cannot imagine trying to drop and engine into the bay AND slid it back into the input shaft of the tranny - that is mounted on the cross member - through the clutch disc spline, couple it to the bell housiing, AND drop it over the motor mounts.
It is tricky enough, for me, getting the tranny and t-case, sitting on and strapped to my tranny jack, with the back of the engine supported with a bottle jack, and massaging the input shaft up to the pressure plate and then push the tranny up to the bell housing at the perfect angles to get the splines on the input shaft to slip through the clutch disc and the tip of the input shaft to slip into pilot bearing!
BUT.... I'm old and slow and as a DIYer I don't get much practice on my Toyotas.... damn things are just way TOO reliable!!
Gnarls.