[Qmulus]

Well, technically the three chain engine from a 2006 Boxster is an M97, which is virtually identical to a late M96 used in the '03 S. I assume that the '06 engine is also a 3.2 from an S. There are some detail changes, like the larger IMS bearing, but other than that you would be hard pressed to find any differences between them. In '07 they went to 3.4L and Vario Cam Plus, which would be a little harder to deal with, but likely still doable.

Seeing that your '03 S and the '06 S both used ME 7.8 engine controls, you should not have issues, with the one exception being that the '06 _may_ use an extra solenoid to control a valve on the intake T. The "fix" is to simply use the intake from the '03, which is interchangeable.

So, use the long block from the '06 with your existing harness , engine controls, and exhaust, and most of the rest from the late M96 would work (should be most everything short of the intake T) and you should be good to go. That said, I have NOT done it myself, and the shop that I saw do it didn't tell me all of the details.

If I were to look for a stock engine replacement for my '03 S, I would definitely look at an '05 or '06 M96 M96.26. Then again I would probably get a late (three chain) 3.6 M96 for my car if I was going through all of that work.

While the engine is out, I would also swap in the 987 airbox.

YMMV