The E4OD would be a healthy trans for it in the "Stang.  The
E4OD is loosely based on the C6 3 speed which was just about
bulletproof.  If you plan on regular thrashing at the strip,
it should be beefed and updated as would be the case with
any other stock trans.  It has been used quite successfully
in certain types of racing - especially offroad racing.  The
gearing is very close if not identical to a C6.  4th is
about .7:1 which means you could easily use 3:73 or lower
rear gears and still maintain a decent cruise RPM.  Again,
Bauman Bros. would be a good source of beefing parts if you
decide to go that way.  I have used TPU here in Atlanta as a
source of parts to build mine but, they are not real deep
into the fullon performance parts for it like some others.

Another possibility for your ECM I had forgotten is that
Ford built a short run of about 248 '93 Mustangs with a 351W
very similar to the Lightnin' engine.  IIRC, they were
conservatively rated around 320HP with near identical
internals and, with no emission certification. They all had
a 5 speed trans as they were built for the race circuit and
sold only to licensed racers (oh, yeah! Torque everywhere by
the bucket fulls!).  Ford Motorsport at one time had the ECM
and wiring harness for the thing listed for service.  For
that matter, Motorsport has been known to pass out some good
tech info for this sort of thing if nicely asked.  Sorry I
do not have their support info number.

Good luck
Lugnut