Hey thanks guys for all the help you provided.
I did manage to solve most of the problem in Preferences, the "Route All Audio Thru Fx" box was checked and that left open loud Fx channels to route audio thru but brings in extra noise.
X2 didn't have this option, and X2 still is just a small tad bit quieter.
@wizard 71, I did open X2 projects, and new X3 projects, but did cut a lot of noise by disabling the Route thru Fx option.
@mosvalve, no Melodyne yet.
@gswiz, couldn't find the bypass all Fx switch. Input echo was off, cutting them all on brings in the noise in X3, doesn't do that in X2 though. In X2 you could cut all the input echo switches on and still get no noise. The Tape sim wasn't on, but I did get it basically sorted out in preferences.
Thanks again for all the help.