I am at the part where you have to choose between letting Legion upload the Reaper codes or not, and the Renegade/Paragon options are grayed out so I can't get both of them to side with each-other peacefully. I looked into this and apparently there is a 5 point scale in order to have both of them.

Geth vs. Quarians
In order to achieve peace between the two races, you need to get 5 to 7 points. These points are based on your ME2 and ME3 decisions. If you have 4 points or below, you cannot achieve peace.
-Rewrote the Heretics (0 points)
-Destroyed the Heretics (+2 points)
-Tali is NOT exiled (+2 points)
-Tali has been exiled/You did not do the Loyalty Mission (0 points)
-Resolved Legion/Tali conflict either using the Paragon or Renegade options (+1 point)
-N7 Mission: Save the Admiral on Rannoch in ME3 (+1 point)
-N7 Mission: Destroy Geth Squadron on Rannoch in ME3 (+1 point)
-Completed Legion's Mission in ME3 (or no peace)

But I have Tali's loyalty, and I destroyed the Heretics so that is already 4 points, plus I did all of the missions on Rannoch so I should have 6, yet the options are grayed out, do I not have enough Reputation or something?

I don't think that has actually been confirmed to be the formula, I think its just the best guess people have right now.

That's all I got.

I assumed it was just 80% paragon score. My first time through I wasn't able to pick the paragon choice, but on my second playthrough with the imported ME3 character, I was.

@Napalm: I'm 99% sure the game doesn't care about the paragon/renegade split anymore, just total reputation. I went almost all paragon and yet had the renegade options available to me each time all the way until the end of the game, and I could also of yelled the Geth and Quarians into working with each other despite my nearly total paragon bar.