Joe,
First I take a bit of offense (kind of) at your comment that the Cat 3208s are dogs. True, they are not fast but they weren't built to be....most diesels aren't The 3208 was built to be durable and they are....unless you have the 425HP versions. I had the 375HP models in my 1984, 52' KhaShing CPMY. That boat weighed 48,000 lbs. I didn't buy that boat to go fast. I bought it to cruise offshore on the West Coast. I wanted comfortable and dependable. She was stabilized with a 3 year old Raymarine navigation system that the previous owner spent $30k on.
My next question....What's the rush? I understand wanting the space for a live aboard but honestly, if you are looking for a boat as a home there are a LOT of boats that are better suited for that task than a Sea Ray....44' or 65'. I bought the boat mentioned above to live on and cruise for 5 years. Going fast never entered the equation. Comfort, dependability, stability, convenience, space, real furniture, a galley big enough for more than 2 people.... These were what was important to me at the time.
Big boats mean big weight and mass. That means diesels to move that weight and mass efficiently....and it doesn't mean fast. It means 10-12 kts at cruise and maybe 20 WOT when you need to get out of the slop quickly. Boating forums, including this one are filled with people wanting their boat to go faster. There is no cost effective way to accomplish that. The rule of thumb I've heard is about $1000/MPH. Yep, wanna go 5 miles per hour faster? Gonna cost you 5 boat units. Re-read post #9 from Go First Class. His response is spot on.
Lastly, if you want a comfortable live aboard why not look around at some other boats. When I was looking, and I've had Sea Rays all my life, I looked at Ocean Alexander. A very well built and solid boat. They have a very nice 44' Aft-cabin, cockpit model. They also made a very nice Pilothouse model in the 50' range. You said you don't like the layouts of the newer boats so look at the mid 90's of other manufacturers. Even the bigger Bayliners (I know, go ahead and laugh) from 46' and up would be better, as far as livability. Then go buy a 22' or 27' mid-80s Sea Ray Pachanga and put your 496s of 502s in that for you speed fix.
Of course, all of this is just my opinion and you will do whatever you want anyway. Good luck. I hope it all works out for you.
Shawn