DorkbotPDX) so I got 3 copies of the design. All 3 looked visually correct so I did some quick electrical tests (resistance between linked pins and unlinked pins) and I couldn't find any pad that wasn't connected as intended or any unintended connections. The one mistake I made was that I made the holes too small (but since this doesn't matter for the surface mount parts and I have female connectors that will fit it's not a big deal - I think I made them 0.032 instead of 0.040). The holes were where they should be (not off center) and very consistently aligned across the board.
If you look at the design there are clear block of elements that make it easier to assemble a few components and the test for function (for example the resistor + led combo on the cpldVccio power lines -> assemble then test with a couple of AA batteries). Then the slightly more complicated ldo/resistor/cap/led combos - do the 3v3 first and after testing do the 1v8 because it uses the 3v3 output as the input source - directly connect the 1v8 enable from the msp430 socket). Then the filter caps and the cpld and then all the female connectors.
I'm still working on the msp430 controller code (time is at a premium when the weather is nice) but I'll post it when it's done.