These mods have been contributed by their original authors in their entirety, and therefore you do not need to run them as they are included in Legacy. Having them in your game with Legacy can mess your save game up. Remove them from your load order and endorse their mod if you haven't because they've done a lot to help make this mod what it is by contributing their work. The Object ID's of course have changed so you will need to reacquire the items, and some items have been reworked or quests added for them in this project.