I've done a few swaps but never an M54 to S52. Is it pretty much bolt up?? Besides having to swap the oil pans etc.

Physical fitment wise the S52 will bolt in identically to the M54. Use the engine mount arms, oil pan, etc - everything from the M54 on the S52 including all accessories. It all bolts up, the engine will then bolt up to the chassis.

I am betting you have a burnt or chipped valve....I have seen a few on M54's...although that usually results in zero compression.

Oil gets in through the CCV over time and eventually burns up the exhaust valve. At least that is the theory...

Regardless, if it is something in the cylinder head, I would slap a good used head on there and put it back in service. The M54-equipped E53 X5 takes a cylinder head or head gasket pretty well. The car stays on its wheels the whole time, and you have good access.

Alright, after some marvel mystery oil in cylinder 6 soaking overnight, no change. Pretty much confirmed the engine is toast. I never saw it coming.. no clue what happened. No warning.
Compression numbers as of yesterday...
Cylinder #1: 168psi
Cylinder #2: 145psi
Cylinder #3: 147psi
Cylinder #4: 100psi
Cylinder #5: 168psi
Cylinder #6: 12psi

So pull the head off.

Three different age coil packs? The spark plugs show some serious ceramic burn through. I think most engines don't get enough rear cylinder cooling. Ram's diesels are notorious for it. Same I6 design.

On the M52TU and M54 the cold coolant flows to the rear of the engine first, then flows forwards to cool the other cylinders. 6 receives the coldest coolant

Have you checked the DISA valve for missing pin?

Yes I have replaced a couple of the coil packs over the years of ownership as needed. But never replaced all. My conclusion was, they either work or they don't. Cylinders 1-5 plugs look very similar, #6 is darker. 1-6 from left to right.

I have not checked the DISA valve for a missing pin. Can you elaborate?