Later model 3.4 in '06 Cayman S?
 

It's starting to sink in I may have to do serious work on my '06 CS 3.4 motor. What I hoped to be lifter noise is now sounding more like maybe wrist pin or broken piston. (I'll still rule out valve problem before dismantling motor completely).

I'm wondering about the compatibility of a later model Cayman S or Boxster S motor with my car; whether I would strip the intake, exhaust, etc and use my old parts, or if I could use the later model parts. I assume I'd need at least the DME from the later car, but don't know what else.

Anyone done this?

Cayman S engines are interchangeable until 2009 when they were totally redesigned.
As long as you stay with the early engines there is no need to touch the DME.

1st thing you should do is have the cylinders inspected with a borescope for excessive wear of the cylinder walls. this can be done thru the sparkplug holes.