The latest Merge Script should rename single. egm (makes clothing fit to NPC bodies) need to stay in. bsa is just textures/meshes they can be unpacked, but certain files such as. Mods that have Navmesh data (which should be.
In general though if you are just using 圎dit to manually merge mods or using the Merge Script there are a couple things you'll want to avoid due to large headache. In principle if you used GECK and ridiculous amounts of time you could manually merge most of your mods down to a couple. A mod can be a single form or it can be DLC sized, so number of individual plugins pre-merge isn't always the best gauge.
There is no real limit on number of mods than can be merged.
