It's interesting that nobody has mentioned MGE XE in this thread. As a patch mod for Morrowind, I now regard it as an essential install.
Morrowind was designed and hardcoded for the older 4:3 ratio screen resolutions that were the norm back in 2002. MGE XE makes it possible to play Morrowind on modern widescreen monitors without stretching and distorting the graphics, as well as increasing the available resolutions choices.
For the issue of dirty references, you can either find online already cleaned versions of the expansions and official DLC, or install The Elder Scrolls Advanced Mod Editor (shortened to TESAME) to clean them yourself. Becoming familiar with cleaning mods in TESAME is worth doing, as not all mod devs have cleaned their mods before uploading to the various mod hosts that have existed over the years, so even after you have a cleaned install of Morrwind, installing some of those mods could re-install the dirty references.
And lastly, there's the choice of either going with the major unofficial patch projects, the Morrowind Code Patch (MCP), or the Morrowind Patch Project (MPP).
The MCP was started in order to fix game engine level issues which could not be fixed by the MPP or its predecessor the UnOfficial Morrowind Patch (UOMP).
The MPP fixes things by installing like a mod, and needing to be activated.