I think I added some mod and it made the continental map too large...because it screwed the sites of the cities, dungeons, etc up and moved their icons over too far. Is their some way to make it fit? Does it have to do with ini? Where exactly to I go to change it if it does?

Which mod?

Nothing in the ini to my knowledge.

The main map things I am aware of are:
1. There are some map files that are stretched (of non standard scale) in order to show areas beyond the standard map regions (Such as the island of Stirk.)
2. there are a couple of mods with esp. files that reposition the icons - in order for them to match up with the above altered maps (the one I am most familiar with is MergedMaps.esp)
3. There are issues (especially when using the above) with running the game with Widescreen resolutions (indexed with a * in the video menus).