What I think:

1.
Skimming the head twice hardly makes over 1mm difference to original.

2.
If the head has been overly skimmed, the easiest remedy is another head.

3.
Even standard carb CVHs with the 9.5:1 CR run over a bar of boost easily with a large front mount IC.

4.
Decomp plate would be my last choice for this.

5.
The original pistons have 7mm of material on their crown. Taking 1mm from the center is perfectly ok. (Don't reduce the distance from the crown to the first piston ring, so only a bowl in the center)

6.
During the setup, surely the AFR was recorded?

7.
Check your plugs. Is it a problem with only one cylinder?

8.
Running a large front mount IC and 15 psi of boost, I would personally like to have a compression higher than standard. If the engine can't handle it, you have a problem somewhere.

9.
Do the compression test.

10.
Have you checked that the ESC-II ecu is doing it's job at adjusting timing with the MAP reading.

11.
You do have the MAP hose connected, do you?

12.
You can measure the head total thickness even when it's on the engine. Compare that to standard or guideline value from manual.