So I measured the eff. tt and I get 57cm which is what Giant lists on website and I am sure they are listing eff. tt since it's a compact geometry/slanting tt bike.
With that said, after raising saddle about 1 cm, I rode 16 miles this morning before work and had no pain. I'm going to ride 30-40 miles tomorrow and see how it goes.
Thanks for all the other tips. For the record I am more of a masher than a spinner, especially when climbing. I try to do my best to keep a steady 90-100 rpm when I can but unless I'm very vigilant of it I don't.