Originally posted by Shingoblade-GSR
Since your car rode well for the first three months with this setup I think your shocks need to be replaced. Another explanation could be that your springs settled and you're riding lower, which may or may not cause the change in ride quality 
This is true in some cases. The shocks will settle in very quickly, especially when using the stock ones, they will sag more than higher quality aftermoarket dampeners.
On that note, if anyone can recommend a good setting for the GC+koni yellow combo I'd be happy to know. Right now when I hit bumps on the freeway (fairly large bumps) going about 65-70 mph, the car bounces really hard and bottoms out upon hitting the bump, and the force actually throws me up out of my seat 
My rebound is set to 1; I assume changing it would help this problem.
Yes...your shocks are set too low. Like qtiger said, 1 and 1/2 turns is a good setting, but even if you decide to adjust them to 2, the ride quality will still be good, it will just be a little stiffer, but still very much within the "tolerable" range. Play around with them and you'll eventually find a good setting that works for you. Experimentation is a good thing.
Also, what perch are your yellows set on? Adjusting that can have different effects on your cars' ride quality and handling characteristics.