So, I decided that I'm going to try and fix my rusted forks and replace the seals before I spend the money on another set. So my plan is to try and sand them down with 2000 grit and fill any pits with super glue, then sand em' again and throw it all together. My questions are, Do any of you guys have any experience with this? and Do I sand up and down the forks or across them?

Yep,
did this last fall, bought an 07 gs with 150 miles on it... needless to say it sat for 8 years without being ridden.  The forks were rusted, gritty, and because of that they destroyed the fork seals. 

I'm not sure about the super glue because you never know how it will react with the fork oil. the oil could break it down eventually. 

But what I did was once I had the forks removed from the tubes, I used a 600 sand paper with a little bit of oil on it gently on any places where rust had bubbled up through the chrome.  To be completely honest I didnt pay much attention to direction of sanding, just did it carefully until I couldnt catch my finger nail over it.  Once you install the forks back into the tubes the regular use of the bike will ensure the forks stay oiled to keep the rust from coming back.

This is just how I did it, not saying its the right way but is is a way, and it worked.  I used brand new K&L fork seals and 700 miles later not a single issue to speak of. 

I did the same thing but used 2000 grit sandpaper. I got it wet with water and went real gentle in circles. Take your time and work the rust spots until you can't feel where they are with your eyes closed. Any tiny pits won't hurt your seals, they will only leak a little bit of oil. If you try the super glue thing let us know how it goes.

I just read that on Reddit recently.... I think Lucas posted it?

Either way, you'll only need to put glue on the areas of the forks that see any forkseal action. And if I recall, you don'twant to sand left & right - only up and down.