There were a number of changes to savedsearches between 3.x and 4.x, see
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.
There were a number of changes to savedsearches between 3.x and 4.x, see
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.