The 390 is a great motor.
My personal opinion is that Chris Craft could have offered this in their engine lineup with the same great success that Interceptor did. Interceptor offered the 390 and the 352 in marine trim (both have external dimensions identical to the 427), and many are still running in Higgins, Trojan, Century, and numerous other boats around the world today as reliably as the 427 version of this same motor is. I think all of the FE motors were (also) solid lifter motors, just like the Chris Craft 427 version of the FE.
There is way too much involved to cover it on an email or forum posting, but hopefully this will give you some idea of what may be involved. Steve Christ has a great book out called "How to rebuild big block Ford engines", ISBN O-89586-070-8. It is a great reference for a project like yours.
Higgins offered a 400-hp version of the 390 in one of their runabouts, so you can see the engine has lots of potential. In addition, if anyone must, they make a truck version of the 390 called the FT, and it has a steel crankshaft, but that would require a different pully setup on the front of the motor, so beware.
The base automotive 390 is a brute, and it is my personal opinion (you should verify) that everything will bolt up to the 390 directly off the marine 427. The cast iron crankshafts on the 390 and the 427 are identical too. The 427 has those cross bolted main bearings, and some reinforced internal cast iron webs, and it is heavily reinforced for NASCAR racing purposes, way beyond what I think is realistic for a boat motor running at a max of 4000 rpm.
As noted, the Interceptor versions of the 390 didnt have the cross bolted mains, and I have not heard of any negative issues with the Interceptor brand, other than the normal run em until they break routine we hear with all motors. You will need to check the marine motor mount bosses, as there may be some fly-cut bosses on the marine motor that do not show up on the automotive version. If those are cut into the 427 block, I think they can be cut into the 390 block too.
Block swapping is quite possible, but it should be left to a machine shop that is familiar with Ford FE motors, unless you are an experienced mechanic.
If you get a reconditioned motor, or a remanufactured motor, chances are youll be getting the LH (automotive) version. Youll need to convert it to the RH version (opposite rotation from automotive) in order to work with your transmission, because it if came from a single engine Chris Craft chances are good that its a RH transmission. You can re-use the crankshaft from your 427 if it is not damaged, or you can polish out the directional wiping marks in the crankshaft at the seals, to be sure the LH automotive crank wont be wiping oil out of the motor. Once these are polished out, you can use a more modern neoprene seal, some of these are directional too. Check with the local NAPA for a 390 main seal, take a look see if its unidirectional or rotational specific.
The LH and RH cranks are identical except for the oil seal wiping marks, and these are a carry over from the old days of rope seals that were used on these motors. They will spin just fine in either direction, but you have to get the wiping marks removed or spinning in the proper direction for oil control at the seal.
In addition to the attention aforementioned about the crankshaft, the cam and distributor drive gears must be specific to the standard or opposite rotation motors. The distributors on a LH or RH motor both spin the same direction when the motors are running, due to the gears on the bottom of the distributor and the side of the cam. The 390 block is a hydraulic block, and attention must be given to the oil circulation. The easiest thing to do is to get a LH automotive long block, complete with cam, crank and all running internals, and to simply swap the direction of the Paragon (you do have a Paragon, dont you?) transmission. That way you can pick up a very inexpensive running motor with a full warranty, pop it in and run with the hydraulic lifters and be done with it. Of course, youll need a new prop, lol.
The 390 block can certainly be used, but there are issues I have noted, and probably some I have not noted, that need to be tended to, and it would be wise to involve someone with some Ford FE experience rather than let someone familiar with the other brand do the work. Im concerned about oil circulation on any side-oiler version too, because those took a specific cam with specific oil grooves in the cam bearings, to assure oil flow to critical components.
If you go with a short block, you can re-use the 427 cylinder heads with the solid lifter rockers, etc., but realize the 390 is a hydraulic cam and lifter motor, so this will need to be properly tended to in order to assure proper oil flow, etc. Hot rodders have swapped back and forth between hydraulic and solid lifters a lot, this is no big secret, but it must be tended to and not taken for granted.
Having gone all the way through that outline, here is an alternative for you especially since you are talking about a single motor application. Many Paragon transmissions (like the HF7D, for instance) are reversible. You remove the cast iron housing closest to the motor, rotate it 180 degrees, and this changes the direction of the transmission. Easier said than done, but easier, perhaps, and with less risk than changing all the internals of the motor. In addition, if you use an automotive rotation, you open yourself up to ALL of the performance cams and intakes available on the aftermarket. If you use the opposite rotation on a FE motor, youre pretty much stuck with the standard cam, as there is no aftermarket for this part any more! It would be far easier to get the economical long block 390, bolt on the marine ancillary equipment, and be done with it. With three hundred and ninety cubes, the lowest power rating youll might be seeing in automotive form with a nice Edelbrock intake and a 600 cfm carb should be in the same 300-hp range as the 427, due to a bit more compression, a little more power on the cam, and better intake breathing. Check into the flycut motor mount bosses.
Hope this helps get you started. These general tips represent my opinion, and everything should be verified carefully before and during the engine building process.
PS: You won't find ANY rebuilt 390 or 427 marine engines on any of the remanufactured engine pages. You will, however, find a good selection of automotive 390 motors that can be adapted, should you choose to go this route. With a new 427 bare block costing $3500, the $2000 or so for a complete running 390 seems to be worth consideration, at least for a moment or two.
Here is an interesting offering, for a 390 with 350-hp and 400-footpounds of torque for $2200. I'm wondering how many owners it would take to actually wear out one of those bad boys, and how many hours of running per year it would take.
Look at this one $1534 for a remanufactured 300 horse engine.
Heres a 390 with 475 Horse Power for $9200. Toll Free: 1-800-267-3940 I wouldn't recommend this one in a boat, but it gives an idea of what the potential of this series really is.