I recently returned to Morrowind and I'd like to have the castle I designed years ago. It's quite extensive and unfortunately I made the decision to merge it with several other mods at the time. Is there a way to remove .esm dependencies from the .esp and remove changes from specific cells in the game world so that I can use only my castle?

You can remove esm dependencies in the Enchanted Editor as well as other tools. I don't know about the second because I don't know exactly what you're trying to do. There may be an easy way to demerge mods but I've never done it myself.

You can open it up in Enchanted Editor, as cdeford said, and chop out the dependencies. Then, if you want to remove changes from specific cells (not specific changes from cells) you can just delete the appropriate CELL records in EE. Save it all and you should be done.