Just to start out, I am not new to gaming at all, been doing it for quite some time now. I even made some top-of-the-line mods in some other games, but never dealt with anything as complex as Morrowind. Anyways, my problem.
I am in the process of making a mod which combines Uvirith's Legacy and Building up Uvirith's Grave, as well as adds some modifications of my own to Uvirith's Grave and Tel Uvirith. Ever since I began I have been encountering weird errors while loading save games, and now cannot load a save game from another save. I need to exit the game if I die or if I want to play a different save.
I used Wrye Mash to clean the saves, and for awhile that worked for most errors, but just today after making some more changes to my mod, I added it into my save with WM, only to encounter some new errors when I loaded:
Local count for script 'CharGenDagger' differs from local count for container item of 'arrille00000000'.
Local count for script 'lightofdayScript' differs from local count for container item of 'ano vando00000000'.
Unable to find Friendly Group Clone 'gp_npc_sara00000000' in Load for REFR '_MCA_companion_elira00000000'.
Unable to find Friendly Group Clone 'gp_npc_sara00000000' in Load for REFR '_MCA_companion_arran00000000'.
Missing object "uvi_dungeon_intruder0700000000" for reference during cell "Tel Uvirith, Tower Dungeon" load.
Unable to find Friendly Group Clone 'gp_npc_sara00000000' in Load for REFR 'PlayerSaveGame'.
Master file topic 'fighting style' has been deleted by 'MCA_Companions_Enhanced.esp'. This may break some quests. You should probably remove the plug-in from the data files. If you are certain you don't need the topic you can resave your game and this message will not appear anymore.
Failed to load spell 'uvi_comp_wb'.
Failed to load spell 'resist fire_75'.
Expression Error Unable to find cell id "Sheogorad Region, Dragon Lair" in script _dragon_teleport_script.

The last error only gives me an OK button, which upon clicking closes the game. Now, I tried cleaning the game again using Wrye Mash, and encountered the error. So then I used WM to remove the mod, Lord of the Dragons, which that script is from. However, I still received that error upon loading my save.

Any ideas as to what could be causing this issue? The only changes I made to the mod was changing some parts in the topics, only words like jail to dungeon, and added about 7 more guards between 2 cells.

All I know is that the more changes you make to various mods and scripts and add into saves, the bigger the problems you will face in the end. The game saves information in an odd fashion that is never fully rectified.

Just today, I had the "local count" error on an item I had created and scripted... and made several changes to in my tester save game. I continued into the game, and the item was gone... I looked everywhere for it, but it was... gone! Then I brought up my inventory, and guess what was sitting in there?

So, I did away with the save and started a new test game. I have 3 installations of Morrowind on my computer... one is just for playing, one is for modding, and one is for testing mods (mine and others) and this works fairly well...as long as I don't get confused about which install I'm in, eh?

Building Up Uvirith's Grave conflicts with Uvirith's Legacy, so maybe some errors are caused by combining the two. There's another mod, Building Up Uvirith's Legacy, which removes those conflicts while preserving the functionality of BUUG. Perhaps if you use that instead it will work better. I don't know if this has anything to do the errors you're seeing, but it's something to try.

If http://www.tesnexus.com/downloads/file.php?id=27588 isn't working for you, it's always the http://www.elricm.com/nuke/html/modules.php?op=modload&name=Downloads&file=index&req=getit&lid=96 you can use instead. May I suggest that you take a closer look to the http://www.gamesas.com/index.php?/topic/1078305-uviriths-legacy-beta-110/ thread (Stuporstar is a good modder). By doing that you might save you some time to you self.

To add to what's already been said (don't make changes to a mod in an ongoing save game, even with MPP and Mash it'll probably cause problems) that last error is usually because some other mod, loading later, has overridden the CELL name.

Chances are that's from Rise of the Dragons or something like that? Anyway that mod needs to be lower in your load order than the mod that's also changing that CELL. No idea what mod that is. You could try a TESPCD "single vs all" check and look for LAND conflicts between the dragon mod and the rest of your modlist.

But, yeah, don't change a mod mid-game and test it out without any other mods loaded (you've MCA loaded too)