it will migrate all customizations however you may have to rewrite all the scripts that are written in crm 4.0 to 2011. As object model of the javascript changed from 2011 most of the scripts written won't work in crm 2015 as it is also crm 4.0 service api end point is deprecated and you have to make sure all scripts are using new service API wherever it has been referenced. Most of custom plugin's and workflows will be migrated to 2015 however its better to verify all the functionalities after migrating. If crm4.0 version does not have any custom plugins/workflow and scripts then migration will be very simple as up-gradation process will update all customizations without much issues.
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