Re: Project Block
We haven't discussed one important aspect; what baseplate thickness are you planning? You should be in the 1mm+ range, possibly up to 3 mm.
Determining pin height is difficult. I know only Cathar has been able to model it, hence the 4mm suggestion (searches will probably hint at 5mm being "essentially" useless). If I was building a block, I'd plan on the long side (both pins, and baseplate), so that I can shave it and see if the performance is better or worse. Of course that means that A) I have the testing equipment and B) the design lends itself to "shaving", which isn't entirely obvious in a pin grid design.
As for CNC, I believe you'll find that endmills are only usefull down to 1 mm (and take an insanely long time). A slitting saw would be more in line. You might want to focus on finding a machinist, and buzzing them on the limits of their capabilities. I had a source for slitting saws but the site seems to be owned by someone else now.
On a side note, the Swiftech Apogee has (apparently) been an exercise in determining the ideal pin density (from previous, albeit sketchy, info posted). Similar designs include the #rotor block, and Hoot's (Overclockers) pin-fin block, neither of which (I believe) included such refinement.
If you make it, and I have my testbench up, I'll be more than happy to assist you with this design.
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