I purchased a 343 new after looking pretty carefully at both boats. From what I had read both boats sailed pretty well and were pretty comparable in most ways. I went with the 343 for a couple of reasons.
Bottom line was that I liked the engine accessibility and the house battery location much better in the 343. I ended up installing a Flo-Scan fuel flow monitor and vacuum gauge on the fuel system, a squeeze bulb to facilitate bleeding the fuel system, and a 325 amp-hr Rolls battery under the berth in the aft cabin. I doubt I could have crammed all of that into the 323.
I really liked the storage volume under the starboard cockpit seat of the 343.
The Admiral liked the headroom above the berth in the aft cabin and preferred the interior layout in the salon/galley of the 343.
I did not have any significant problems with the mainsail furling system. All in all I was very pleased.