You can take a look at this article for information on upgrading your JavaScript:
Upgrade Scripts to Microsoft Dynamics CRM 2011
It's hard to gauge how long upgrading code would take - depends on the amount and complexity. Then figure in additional time for testing. Tthere are also tools available to help with code upgrading - Dynamics
XRM Tools
Assuming you are moving from 32 bit to 64 bit servers figure in time to set up the new servers and get everything installed.
Depending on the size of your database, the actual upgrade could take several hours to perform.
Also keep in mind time to upgrade any Outlook clients from 4.0 to 2011 (not required right away) and also any additional user training.
CRM Upgrade Best Practices
Jason Lattimer
My Blog - Follow me on Twitter - LinkedIn