Re: Connection takes hour to establish.
328 feet (100 meters) is the longest that any one run of cable can go without losing data integrity. Since you are only 20 feet below that, I would think that the signal is just getting weaker because of the length of cable. I would suggest putting something like a switch or something in between the Cisco 2650 and the linksys switch to make the signal stronger.
EDIT: Cat 6 will NOT help in this scenario.
Official "Birthday Man" of CF.