Scott1e i have the 4th gen accord like yours too but i fitted an intake setup i bought at autobahn for i think around under 100 dollars. Which includes pod plus metal pipe and fittings.

I pulled out the old stock box but i still left that lil box next to the battery on the left the one u mention that had a pipe that leads into the air filter box. Theres a vacumm hose that ur scared might damage something if you dont connect it back up yeah?
Dont worry, i drove my car around and didnt notice any problems, i think its vacumm line number 8 if my memory serves me right. If you pull it out, just seal that hole that comes out of the fuel injected. Cut a small piece of hose and at one end put a screw into it and then shove it back to seal the hole?

If not just buy a long vacumm line and connect it back up.