You should be able to get a good 350/350 with that budget. They are indeed the same boat, just a model year designation. Ignore the mountains of discussion about the hull extension (bustle,) if the boat doesn't have the fix use that as a bargaining chip, but don't worry about it.
You will also find much discussion about the Cat power on some models. The 3126 is a fine engine and ignore any stories about this geing a "bad" engine. Later boats had the Yanmar's which have proven to be a good choice of power for these boats.
Single / Dual is personal preference and with a little objectivity on how you will use the boat the single option should win. I believe all the single engine 350/390" had bow thrusters, and a worthwhile upgrade for some units is newer higher thrust thruster props.
The generator placement is a pain to live with, a real shoehorn job under the cockpit, but like all things a compromise.
This Mainship is a very popular boat and there are plenty for sale. I like the layout and the flybridge is awesome for this size vessel. Stairs are big + too.
Good Luck and maybe consider looking over the Yahoo Mainship owners site, wealth of 15 + years of knowledge over there.