While putting fluid in my 5 spd, I dropped the 3" piece of vacum hose I was using to get the fluid in, in the trans. Do I need to disassemble the trans and remove it, or just not worry about it and let the trans eat it?

Stupid is as stupid does!!!

 

Pull the drain plug and see if it follows the fluid to the drain hole where you can retrieve it. I would not leave it in there, it may get chewed up and get caught in the bearings.