This thread may be super old and all, but I'm going to post what I know for the benefit of people searching this topic in the future (I came to this thread via Google search, for instance).
During a swap of a tranny and torque converter from an '05 into my '07 (long story, it was a straight OEM replacement for troubleshooting purposes), I found that the t/c and flexplate designs had changed between those years. The four nuts on the t/c were both a different size ('07 used a 1/2" socket, '05 was a 15mm socket, neither nut fit the other year t/c), and spaced differently (see pics below). As a result, the holes in the flexplate are also spaced differently.
'05 torque converter:
'07 torque converter:
For clarification purposes, both sets of parts came from '05-'09 4.0L V6 Mustangs with automatic transmissions.