I want to add +100 magicka to my Dunmer, but am not comfortable adding any magic mods to the mods I am already using yet. Can I do this in the console or something without it messing with any mods I might use in the future?

try:
player-> setmagicka xxx

Actually I do believe that even though it is set higher than 100 with the console command, it doesn't give any extra benefit. I tried this with acrobatics and my jump seemed to carry me the same distance as 500=100

No, changes made by the console act true.
Meaning that they act the same as if the stats were gained in a normal manner.
Drop all your gear... now try.
If you used the command correctly, setting your Acrobatics to 500 will be different than 100.

Thank you Pluto for clearing that up, I used PCsetskill "Acrobatics" instead of player->xxxxxxxxx, GameFaqs needs to check their console commands :/

Gamefaqs is not a reliable source for MW info. (in my opinion)

Use the http://www.uesp.net/wiki/Morrowind:Morrowind

This I have discovered, and UESP is now on my third tab

There used to be a trick with casting Soul Trap on yourself to fortify stats. Whether or not it still works I couldn't tell you, it's been a few years since I've played Morrowind.

you can add a birthsign power to increase magicka, that's the least intrusive. the setmagicka will be lost once your character is hit with an intelligence drain or boost.