Is there a chance that stock 2011 96" cylinders/pistons will interchange with stock 2001 88" cylinders/pistons? If not, what is different between the two motors.

 

Stock cylinders are the same (3-3/4" bore) ... but, the pistons are different ...

The 96" is a stroker version (4-3/8" stroke) of the 88" (4" stroke) ... so, the piston skirts and the hole for the wrist pin are different on the pistons and are not interchangeable ...

(Same reasoning applies for the 103" pistons vice 95" pistons ... they are both 3-7/8" bore, but different strokes ...)

R/
'Chop

 

...............but you can bore those 88"s to 98".
Scott