Is there a reason why you need to swap out the input and output shafts?
Just eyeballing the pics, it looks like the both are close - the output shafts look pretty damn close to me.
Is it the spline count?
Might be cheaper to go with a custom driveshaft?
If it's input spline count, then go with a "custom" clutch set-up?
As for special tools...
For the nuts, you can cut a socket in half and weld them back up on a length of pipe.
For a super long puller, someone had the ingenius idea of using a regular puller but using special cut long length "arms" to extend the pullers reach - kinda hard to explain, but if you seen the pics, you'd understand...
EDIT: Courtesy of
FC Zach...
http://www.rotarycarclub.com/rotary_...ghlight=puller
-Ted