I've been thinking about this some more and decided to post some thoughts that although somewhat influenced by my "leave it alone" philosophy, has what I believe (hope) are some practical views.
I'm not seeing where there's really any useful space in the "new" eng room to be gained by this project. You will loose the storage capability of the bulkhead walls that are currently between the eng rooms and passageway since they will be gone. You will add the walls/doors front and rear but with the doors there, you will not have any added storage space on those walls to replace what you lost.
THe space between the engines is not usuable to any extent because you have to be able to move between the engines anyway using the same space that the passageway/access panels currently use.
I guess if soundproofing the eng room is a big issue, it may be easier to soundproof one larger room although I'm not sure that's acoustically correct. It might be more sound-effective to isolate the separate rooms - but I'm no acoustic engineer so I don't know.
You will also be losing space in the salon with whatever type of stairs you plan to install.
So unless I'm missing something, it seems to me that you will be losing usuable space both in the living portion AND in the eng rooms.
I have the tools on our 53 to do virtually anything including overhauling the engines and spray-painting. I have 3/4" drive socket sets and breaker bars in addition to 1/2, 3/8, and 1/4; all the appropriate wrenches, tune up tools, electrical tools, etc, etc, etc. Most of the tools are in the eng rooms without obstructing floor space or work space.
The primary "space saver" I have taken advantage of is the top of the intercoolers. Mounting a "shelf" on top with a three-drawer tool cabinet mounted on that gives a large amount of storage that doesn 't obstruct anything. If you examine the IC mount, you will see that it is extremely substantial - a tool box on top will not cause any distress at all. I also have some baskets mounted in the ERs to hold various liquids/adhesives/whatever.
I really believe that you will not gain anything spacewise by undertaking this project. I think Hatt pretty much delivered all the usable space available in a boat this size. The 58 LRC has, IMHO, exactly what you're looking for. Whether you are interested in one of these, I don't know but it wouldn't hurt to take a look. THe downside is that the LRCs are a lot more expensive than a 53 (or the standard 58). We would move "up" to the 58LRC in a second but it's out of our price range.
In any case, best of luck!