Crankcase pressure

[bwake]

2KS Specifications and there are some differences here:

Liner Projection 0.06 to 0.18 mm ( 0.0024 to 0.0071 inch)
Maximum Variation in Each Liner 0.050 mm (0.0020 inch)
Maximum Average Variation Between Adjacent Liners 0.08 mm (0.0031 inch)
Maximum Variation Between All 6 Liners 0.100 mm (0.0040 inch)

If a liner does not meet the recommended cylinder liner projection specification, check the following parts:
The depth of the cylinder block bore should be 100.00 ± 0.03 mm (3.937 ± 0.001 inch).
The liner flange should be 100.12 ± 0.03 mm (3.942 ± 0.001 inch).
If the dimensions for the liner flange do not match the specifications, replace the liner. Then repeat the liner projection measurements. If the dimensions for the depth of the cylinder block bore do not match the specifications, replace the cylinder block. Then repeat the liner projection measurements.

I'd check the block bore and liner flange measurements listed above. If those are correct, you should find the final protrusion to be within specs. If you have a ring compressor, I'd say pull the pistons and drop them back in after everything is set to your liking.