Andi,
It sounds a bit obvious but are you starting from the Morrowind Launcher? If not then this is the place to ensure the mods and the Tribunal and Bloodmoon expansions are in and running. See my reply to VickyD if you want to run the launcher from the menu bar.
I have quite a few mods running including the 'better heads' and 'better bodies' ones (a warning about the latter - if you kill someone and you take their clothing the results are (ahem!) very realistic) and other mods to improve textures, increase the number of trees, improve the night time lighting in the towns, etc. As it is a matter of personal taste the best way to try mods is to look at a site such as http://www.mwmythicmods.com/telesphoros.htm which is kept pretty much up to date, categorizes the mods and provides links. The fix for the journal issue was in one of the game patches rather than a mod (I think it was the original 'Unofficial Patch' by Thepal but I could not swear to that).
It is very tempting to add lots of mods but some can impact the speed of play so it is worthwhile including them one or two at a time. Also be prepared for Morrowind complaining on the start up that certain files for the mod can not be found - it usually indicates that the file has been removed by another mod or it is not in the expected sequence. Morrowind will usually carry on if you tell it to and the fix can normally be found somewhere on the web.
Hope this is of some help.
