I am a fairly new mod user and have a question or two regarding their removal. I read somewhere that even though you uninstall a mod that references to that mod will still be in your saved game files and can cause issues. Is this true, or does this only apply to scripted mods? And if so is there a way to clean an unwanted mod from a saved game?

I was thinking about looking into tes5edit hoping for a solution before I go willy nilly getting rid of no longer wanted mods.

Yes to the first question, and no there's no ssafe way to clean an unwanted mod. Be aware however that the main problem is for mods using plugins, particularly scripted mods. Texture and mesh replacers can be removed safely. TES5Edit will not clean your savefile; you'd need a hex editor for it, and it's not a good idea to mess with the savefile. You'd be better off reverting back to a save made before you installed the unwanted mod, which is the only way to make sure your game is free from that old mod...

Here's the thing. I have a character that is around level 62 or 63 and I started having problems with dawnguard causing me to crash to desktop. Well I went through all my mods and turned them off trying to find the solution to my problem before realizing I was having an issue with dawnguard itself. I pretty much retired that character due to what I thought was bad mods or a mix thereof. Now I have rarely had a CTD and am wondering would it be safe to bring that character out of retirement even though I no longer have quite a few of the mods associated to that particular save game file or would I wind up having more issues than it is worth?