JD Ray, there's lots of good input above. A few things from my perspective, some of which may repeat some of the other input. Rather than hit your specific questions, many of which have been addressed I have just a few additional comments.
1) You didn't mention your actual price range and size target but one thing to keep in mind is that maintenance costs are not linear with length. A good piece of input I got from a professional was to expect maintenance costs to double every 5 feet.
2) Where you boat and how you use it drives the configuration. We love the tri-cabin design as it provides good separation from guests and a large master. But mostly it comes down to personal preference. For this you just have to look at various boats and I'd suggest chartering a couple.
3) Be open to looking at a variety of boats. We purchased a boat that wasn't in our initial target list. We started out to buy a Grand Banks 42 and ended up with a Tollycraft.
4) The main benefit of twin engines is the 'security' of powertrain redundancy. I can tell you that I've been on a single engine boat when something failed. We really wanted twins when we bought our current boat only for that reason. But it doubles engine maintenance cost. In many ways the ideal, for me, would be a single with a 'get home'. A bow thruster would be nice but frankly, it isn't that hard to learn how to manage a single.
5) Flying bridge. I wasn't much interested in the flybridge when we bought. Since we've had it I've only once used the lower helm station. The visibility from the flybridge is great, we have a full enclosure so it is 'all weather', and I was surprised how subdued the motion was up there.