Am jealous! This is the build I want to do - stronger bottom end, 1/2 pt less CR, _keep the squish band_, coated pistons fit close enough not to slap & burn oil. Big piston clearances are just lazy - oem's don't do that even on 7000rpm engines, you just have spec the piston right.
For a really extreme build, I'd like to see someone use a VGT such as Holset's. You could program whatever boost curve you want rather than trading top end vs driveablity via hardware.
One would prolly have to mix'n match turbine and compressor sides + prep the turbine to handle more heat since the original design is for diesel. They're meant for trucks that run WOT much of the time so they might handle a gas passenger car app better than it looks on paper.
Those smaller holes are secondary transfer passages from the water jackets around the cylinders to the head. For HP applications they are usually sized a bit smaller to control coolant flow generally to restrict and slow it down to improve heat transfer around the more critical areas. The main IN/OUT passages from block to head are "normal" sized.