You should number the pixels in the order that they are found in the string. The first pixel after your controller is '1', the second is '2' and so on. So your pixel placement may differ from mine based on how you laid down your pixels.
I found it easy to take a picture of my coroflake -- ideally after you placed the pixels and before you glue down the cover. Then use this picture as a background into excel and start numbering cells on top of the pixels.
I did mine in fairly high resolution... a 100x100 grid so that I'd have my custom model fairly precise. I'd show you with a picture, but it is hard to resize the grid to where it shows my point.
as far as my placement, i started with the top arm, and the left-most 'bud' and numbered around that arm in counter-clockwise fashion, continuing down the the center of the flake (this was 1-10)... then continued with my string of pixels to the next arm in counter-clockwise fashion. i chose this order and starting point in an arbitrary manner. with a customer model, the order is not important as long as the numbers match up to the order on the string.
my order did lend itself to models (2) and (3).
btw... with 9 coroflakes I used the manual string channel assignment... and with the model (2) I combined the 9 flakes with 5 arms into a single model... 45 arches.
similarly in the 50-pixel arch, i has a single model that had 9x50pixel arches. this allowed the 9 flakes to work in unison.
...just found the original picture I used in the discussions:
