The lude shifter is shorter, although throws aren't reduced it looks cooler and feels much nicer.

If you can do the work yourself then do the auto-manual. You have a donor car for parts, all you need now is the time, you seem to have the knowledge. Maybe on a real new car it would be worth it. Some of us have cars that are in really good shape that would be hard to find in a manual. There are not many 4 door 5sp EX Accords out there to begin with, now find one in good shape when they are 8-10 yrs old.