2003 non-S motor + trans (5-speed manual) with 2002 S motor + trans (6-speed manual)
 

I have a 2003 Mini manual 5-speed non-S with inoperable transmission. I'm told the transmission + flywheel should be replaced. The total for this is approx. $4,500 providing an unlimited 2-year warrantee.

In lieu of the above and potential alternative presented to me was a motor+transmission swap: install a 2002 S motor + transmission (6-speed). I would like to explore this alternative and see what the general sentiments are in terms of this option being feasible and the additional costs beyond the motor + transmission.

Thank you in advance.

There's FAR FAR more involved then just "swapping" the motor/tranny the supporting electronics/sensors/wiring harnesses ect all would need to be moved over into the non S
You'll need an expert electrical person to even think about the swap ,,, Mechanically the swap isn't tat bad pretty much remove the old in with the new ...
Battery will need to be swapped to the rear of the car Ect Ect ... These are just off the top of my head I'm sure there are tons I'm forgetting

I have a 2002 with the 5 speed manual transmission, has anyone switched the trans from an S 6speed manual, I know I would need the shifter obviously, what about the flywheel and clutch assembly? The bell housing should bolt up to the block ok? ant help would be appreciated.
Thank you for the help, this is a nice car with a cosworth cylinder head, the owner is considering what to do next.

It can be done. Take a look at this thread and specifically this post here.