Welcome to sailing, a sport where there is no one right answer. From what I know of San Francisco you are sailing in one of a three venues packed into one. The upper Bay is a prevalently light air venue, the lower Bay has high winds and currents, and then you are out in the Pacific. Shoal Draft is not as much of a problem as it might be in Florida for example.
Your questions are interesting in a odd sort of way. You clearly seem to be interested in how fast this boat will be with these various options. This is one of those ''is the cup half full or half empty?'' sort of a st of questions. You are starting out with a boat that does not offer all that high performance but live in an area where performance can be rewarded with an easier time against the currents and faster offshore passages. You might reasonably argue that you are picking out a medium performance boat, so why worry about the impact on performance of these various options, or you could argue that you are starting out with a limited performance boat and so anything you can do to enhanse performance is doubly important. It is not for me, or anyone else for that matter, to tell you whether it is right to opt for the ''half full or half empty'' option.
When I mention relative speeds, I will be quoting from PHRF handicap racing ratings which are supposed to equal out difference in speed between different boats so that they can race in the same race. PHRF assigns a rating to a boat in second per mile so it is pretty easy to determine the speed difference. Ratings are assigned regionally so rating practice varies with the Regional authority which is why I am quoting ranges rather than a specific number.
Anyway a fin keel will generally offer more stability and better pointing ability than a wing keel and be much easier to extract from the bottom should you run aground. A fin keel generally has less drag and so is faster. PHRF says a Wing keel is 6 to 9 seconds a mile slower. A fin keel usually has better dampening and a lower vertical center of gravity and so should generally offer a more comfortable motion in the short chop of the lower Bay.
Three blade props make more sense on heavier displacement boats than the 381. They should not be necessary for a lower drag boat like the 381 and would have a more adverse effect on sailing ability on a boat like the 381 than on a heavier cruiser. Assuming that Catalina left a large enough tip clearance for the proper diameter two blade propeller, a two blade should be more than adequate. According to PHRF a three blade vs two blade is a 3 ro 9 second hit.
Folding (vs feathering) props are comparatively inexpensive to buy and maintain. They offer better sailing performance than a fixed prop. PHRF says a folding prop offers a savings of 3 to 9 seconds a mile over a fixed prop. Folding propellers are a bit less efficient when motoring. (I personally would probably do a two blade folding prop.)
Feathering propellers have a similar drag to a folding prop but require a little more maintenance. They generally open and feather more reliably than a folding prop.They generally are more efficient when motoring. They are more expensive and probably are not necessary for a boat like the Cat 387.
In mast furling takes a significant performance hit. Within the past few years there was a study of how large a performance zapper in-mast furling really is. The study concluded that combined loss of performance for in-mast furling cost roughly 20-30 secs per mile depending on the installation and sail features. That is like the difference in speed between this boat and a 30 or so footer. In other words that is a really big hit.
The thing about in mast furling is that it takes its hit at both ends of the wind spectrum. The light air part is pretty obvious, less sail area and a large mast area sending on more disturbed air. The heavier air issue is more complex. Here the increased heeling that comes from the extra weight aloft and the larger mast section combined with poorer sail shape and the tendency for the leech to stretch and so flutter really comes into play. It would be the last thing that I would want in a venue like S.F. Bay.
In boom furling offers similar performance to a conventional mainsail setup when fully raised but when reefed the lack of sail shape control means that you do give a little performance away in heavier going.
On a boat like the 381 sailing in S.F. I would probably go two line slab reefing lead back to the cockpit with with two rows of reef points. This allows the fastest on the fly reefing, the best sail shape and the most reliability at the lowest price.
While the mainsail on the 381 is pretty small for a 38 footer, if you felt that you needed sail tidying gear then I would do something like a Dutchman or a stack pack.