Replacement of the clamp bolts (y-pipe to flex) isn't a bad idea, for some reason the Phazer has a different style that uses a coated shoulder SHCS rather than a bare std. one. I would go with those if possible, order both just in case they don't fit for some reason. As for the flex to block bolts, I would only replace if damaged or corroded, and I would use the OEM ones as they are the exact length and have the shoulder.
I always coated mine (threads) with Never-Sieze, and it made the following years disassembly much easier. Never had an issue with them comming loose either. While you are using the copper andakw think this should be the last time in there I wouldn't bet the farm on it. The pipes will eventually go.