I'm writing a script to go through and run commands on tons of Cisco switches, the command in question takes forever to finish running, we're talking 20 minutes, and I unfortunately I have to monitor it and log when the command finished processing. I'm using perl, particularly the waitfor() and print() functions of the Net::Telnet class. How can I disable the timeout once I get to the point that I would run the for-mentioned 20 minute command? Mind you I still want it to timeout initially so I know if I'm trying to connect to a bad hostname or am using the wrong credentials to authenticate.

Is tons * 20 minutes greater than (early_ retirement_ age - current_age) * 2000 * (60 / 20)?
I think that you should investigate a methodology that allows you to upload a script and then some time ( 20 minutes?) later check to see if the upload was successfully executed.