Migrating x-cart 4 to 5

We have an x-cart version 4 working on our old server and we like to upgrade it to version 5 and move it to the new server. Need to upgrade the data and move it to the new cart, but also need to make sure that no malware that may be on our old version, will not be migrating to the new cart. So we will need also to check the data at the places that have a potential for malware.