The main question to start with is of course, did the game run well in the beginning? If it did, the problems are most probably mod related. A good method is to disable half of the mods, and check if it works --- if it works, you know the problem is with the half you disabled... if it doesn't work, enable the disabled half, disable the other half... and so on. Step by step, by disabling / enabling, find the problem.
There's usually a crucial point = like one mod that causes trouble. You just have to find out which it is. You could check for information about mod conflicts, or you could post a list of your mods here: someone may notice conflicting mods, although I can't make any promises. A very simple tool is ReOrder Mods, http://planetelderscrolls.gamespy.com/V ... tail&id=43
If you're running 64 bit, Morrowind is known to have issues with it. You could give info about your OS, and some system specs too.
I may not have provided any clear answers, but questions are certainly the way to them? And I wouldn't disclose another way to solve it all: save your saves, uninstall everything, do a registry cleanse, do a HDD defrag, install everything, copy your saves to Morrowind, and start again with one mod after another --- you'll get a heck of clickings, I HAVE warned you, but oftentimes the radical measures are faster than trying to "find the fast and easy way".
"Feel free to ask and comment".
And definitely, best wishes.