The bike will sit higher in the front, but you can run the front springs and damper rods without doing the rear shock extension. You are going to notice that the back is quite a bit softer (stock) after you make those changes to the front suspension. Hope that helps!
For the 2013-2015 CRF110 the manual calls for 180cc of oil. Typically 5w oil is used, but if you want some more resistance in the forks you can bump up to a 7.5 or 10w fork oil.
Sorry for the late reply....I don't have a set of forks handy, but typically those are a 4 or 5mm I believe. Is the head of your bolt compromised at all?
I'm not sure what that means either. These forks are pretty primitive in how they are put together and work so there's not much you can mess up with them.