There were a number of changes to savedsearches between 3.x and 4.x, see
http://docs.splunk.com/Documentation/Splunk/4.0.10/Installation/Whattoexpectwhenupgradingto4.0#What_...
In addition, the arguments to scripted alerts were altered, so if you have custom scripted alerts, these will need to be changed.
There may be other details.
However, I would not recommend deploying 4.1 at this time. Splunk has released 2 major releases since then with countless bugfixes, many improvements in workflow and performance, etc. There is not much reason to build out 4.1 instead of 4.3.
