Looks like someone who used to be automatic and is now H22 and 5sp should answer this question.
1. 5sp kicks major ass and it'll run you an extra $1,300 in parts and labor.
2. Do not use the accord auto or 5sp tranny. The gearing sucks on the 5sp accord for the H22, it'll be worse with auto and it won't hold up.
3. Only swap unless your motor or tranny is junk.
4. The JDMH22s came with automatics. The swaps are cheaper than 5sp swaps and the automatics are much better than the crappy Sport shift tranny.
5. The fastest 1/4 mile for an auto JDM H22 in a 94 EX 4 door was a 15.1 with basic bolt-ons. A 5sp with practice should be a high 14 second car.
6. Nobody has swapped the SS tranny from the 97+ ludes as far as I know and I wouldn't even try it since they are crap.
7. Did I mention 5sp kicks ass.