Caltric parts are hit and miss. Some are good, and some are not. I will not buy their electrical parts anymore, because in my experience they have been either cheaply made or are not made correctly (their coolant switches are made backwards to what the OEM parts do).
I have no experience with a Caltric carb yet, but I have experience with a few Chinese carbs....and like many other people, have found them hit or miss. Some have great luck (and have posted on here stating that), while others never can get them working right.
With your engine, I wouldn't worry about the compression until you get it running again. If you getting 120 psi now after sitting for months, that's not bad.
It's a good chance your valves are leaking and will need a lapping. The 2002-2004 660's were known as oil burners, and it was mainly due to the piston rings. Yamaha used different rings in the 2005-2008 models that cured this issue.
If you feel you need to open the engine up after getting running first, then I would do a new piston, rings, valve seals and lap the the valves. You'll have very reliable, excellent performing platform that will last for years.
Btw, believe it not not, OEM will be your cheapest route in the engine. Yamaha engine parts are surprisingly cheap compared to how they price their accessories.