So I finally got my heat-sink this weekend, and mocked it up tonight. I was using CJerome's layout, but found I was having issues getting the measurements to work in a way I liked (my bad math is all). So I redid the measurements and spacing to try and make it as even as possible, this is my end result (with some numbers for anyone else following along). I also plan on using a drill press to tap all 48 holes and get them mostly straight, then I have the fun task of tapping all 48 holes. . .
Heat-sink measurements:
14" L x 7.25" W (7.29 exact).
The 14" corresponds to left and right, and the 7.25" corresponds to front to back.
I measured in .75" (3/4") from both left and right sides. I then measured in .625" (5/8") from both front and back.
I then drew lines in 2.5" increments from left to right and 2" increments front to back (this gave me the most symmetrical grid I could work out).
I then measured my star boards and found that .75" spacing set the screw holes perfectly for my button head hex drive screws (4-40, 1/4" L). I then centered the .75" on each junction of the grid for the 4 inner rows, left to right.
The two outer edges left and right required different measurements: I started on the same front grid intersection, but then measured .875" (7/8") from the last screw hole mark, and made the new set. So screw holes set at .75", measure .875", screw holes at .75", measure .875" etc. This spaces them evenly and leaves space for the fan cutouts.
Since I didn't want to pull my hood apart to check the fan spacing, I simply made the same cut on both sides--from left (and right) measure in 1.5", and from the back forward measure in 1". You now have a nice little rectangle to cut out.
Also the center notch--Measure in 6.625" from either left or right along the front edge of the heat-sink, and draw a box .75" wide by .75" deep (I plan on just using a large drill bit to remove the box--a .75" drill bit if I can find one easily enough).
Here is a pic just to help make sense of my ramblings. I did one test hole just to see what I was up against--and of course I didn't have a tap driver so that made my life difficult for a while--but once finished the screws tighten down wonderfully.
The black dots are where I will be tapping out holes for the screws. I also plan on pre-cutting and tinning all the ends of the wire for the leds (the blue's are mocked up on the paper) just to have smaller bites to chew on each step.

To anyone who knows: Can I use the fiber style washers they sell for computer stuff to insulate my screws from my star boards? The nylon ones I got are too big (wasn't paying attention to OD size) and I can't find any nylon ones that are the same size as my screw heads.