I have ridden a giant ocr2 for the past 8 years or so. The bike fits like a glove and I had a fitting done in it. I recently bought a cannondale synapse. On paper the measurements are all the same other than the head tube which is .5 cm longer. When measures the top tube of the new bike, it mashed one cm smaller than the giant. The cannondale uses compact bars where the giant has a traditional set. The distance to the tops is 2cm greater on the cannondale, but distance to hoods is almost identical because of the compact design of the new bars. Everything seems to be dialed in properly according to my old bike measurements. The problem I'm having is I don't feel as comfortable on the bike. My left hip in the crease seems to be closing up to much, and my lower back on the left is getting a little sore. The saddle heights Are he same, I can't figure what adjustment is necessary in order to make this go away. Is this a saddle height issue?

Are the crank arms the same length between both bikes?

Yes. 170mm.

Same pedals/cleats? It does sound like something related to saddle position. Check saddle fore/aft on both bikes by dropping a weighted string from the center of the saddle and measuring the distance from the BB to where it crosses the chainstay.

Cleats pedals the same. Different shoes. I don't get it.

Is this indicative of too high / too low saddle or too far back / too fa forward saddle? Could this be foot distance from pedal spindle...?

I think it's saddle fore/aft. From what I could google, your bikes have slightly different seat tube angles, and the seat posts may have different amounts of setback. This means simply matching up the 'right spot' on the saddle rails will not produce the same saddle fore/aft in relation to the BB. Try the 'plumb bob' method I described above and see how they compare.