I'm surprised it's so simple to do with the Hondas. I own a Subaru Impreza sport wagon that I was looking into turbo-charging and doing a manual swap. Turbocharging the usually complex-to-work-onboxer engine is cakework it seems compared to the ammt. of work required to complete the auto-manual swap. Lots of wiring, differential work, looked pretty intense. Possible, but intense.

I had an automatic Civic that I wanted to make manual, I just sold it and bought a 5spd. You probably wouldn't lose a dime so long as your auto is relatively stock... 5spd's can be had for less than an auto of the same model, depending on your location I guess. Lots of commuters in my area, so was simple for me.

Anyways, good luck, do what you think is best.