I agree with Wolf about those saves and I know that you can't rely on the quicksaves (save=F5 and load=F9 both default) when you reload a gamesave, because I tried that last year and this is what I did. I manually save the game through the in-game menu and select the quicksave when I was outdoors in Balmora with a lot of wandering NPC's between the pawnbroker and Ra'Virr trader. I reloaded a gamesave via the F9 key 10 times in a row and only 2-3 times I had a CTD, but if I use the F5 key to save my game and then reload it I had only 4-6 successful game loadings. That being said I recommend the quicksaving feature not be to used when you have wandering NPC around nearby especially in Vivec or in Mournhold with more than 350+ gamesaves in the \Morrowind\Saves folder. Another thing that you need to remember about a modded game is the installed mods needs go through the initialization before you do anything (casting spells, use of enchanted items, movement, use of potions etc...), so just wait a few seconds once a game has been reloaded in Morrowind.
However, oddly, there has been some discussion here before that seems to be more or less proven that using the quicksave does help stabilize your game...
as long as you don't load from it. In other words, quicksaving frequently while you play, for whatever reason, seems to reduce crashing. BUT, you need to also manually save whenever you think you might need to quit the game and reload. Every time you save manually, you do best to create a new save; I actually have a backup program to save the last three or so manual saves I make, and then I just delete the rest when I'm done. It might help to make another folder in another location you can move your backup saves to, as well; I have found that the more individual save files I have in the Morrowind saves folder, the less stable the game gets. Again, I have no explanation for it, but I seem to recall some testing a year or two ago from several people reliably getting similiar results.
You might try creating a new character as well. If you have a problem with both characters, it's probably something with the game; a mod that actually adds something small to Ebonheart after all, or your MGE/MWSE setup. If you don't, it's probably something to do with the save. It is possible that if you removed a mod, it corrupted your save, particularly if you haven't been cleaning your saves with Wrye Mash and/or you'd already been to Ebonheart before you removed the mod, even if that mod had nothing to do with Ebonheart.