Vij -
Your best bet is to remove all custom indexes, sp's and triggers from a copy of your 4.0 source and try the upgrade -
It's possible some of your custom work references fields that are modified by the upgrade process. - and some may be dependent on fields that do not exist in 2011 (such as the deletionstatecode fields.)
Once you've upgraded, migrate your custom code to 2011 and test each item to ensure compatibility with the new platform.
(Scribe is a useful tool for moving data in and out of CRM, but it does not perform the 4.0 to 2011 upgrade for you.)
Scott.
Scott Sewell, CustomerEffective | http:\\blog.CustomerEffective.com | Twitter:@ScottSewell