Regarding your plans, I offer these comments:
The wood used by Boston Whaler is very high quality. Usually there is no need to completely replace the wood unless it is in horrible condition. Cleaning, sanding, and refinishing the wood can usually restore the wood to its original appearance.
There is no basis to "assume" than a 1978 Boston Whaler boat will have a interior foam core that is water saturated. I also doubt that a reasonable assessment can be made from the small image of the hull at an unusual angle as seen in Figure 1 above.
For advice on determining if a Boston Whaler boat has water in the interior, see the FAQ.
Regarding the location of the FAQ for the boats: the FAQ is in the REFERENCE section. The REFERENCE section in in the WHALER section, The WHALER section is linked from the top page of the website. The website has extensive resources that are not in this forum. Please become familiar with those resources by browsing the WHALER section.
Here is a link to the top page of the website:
http://continuouswave.com/Here is a link to the WHALER section:
http://continuouswave.com/whaler/Here is a link to the REFERENCE section
http://continuouswave.com/whaler/reference/Here is a link to the FAQ
http://continuouswave.com/whaler/reference/FAQ/And here is a link to the FAQ answer regarding water in the hull:
http://continuouswave.com/whaler/reference/FAQ/#Q3The FAQ contains well-researched answers to many frequently asked questions.
For example, questions about how to repair damage to the hull are answered in the FAQ. See
http://continuouswave.com/whaler/reference/FAQ/#Q5I caution against making drastic changes in the design of any component in a Boston Whaler boat. Boston Whaler boats are highly regarded for the simple but elegant designs they employ, and home-made components that are added to a Boston Whaler boat should harmonize with and continue the general style of the original components.
Empty fastener holes that are above the water line and not in the cockpit deck are not likely to be problems, but repairing them is appropriate. The holes can be filled with a resin and filler mix with appropriate color tint. Holes in highly visible areas should be top coated with color-matched gel coat resin. Holes in inconspicuous areas do not necessary need a perfect color match finish. In some cases a unnecessary isolated hole can just be filled with an oval head screw and dress washer.
Empty fastener holes in the cockpit deck, particularly in the stern or in a sump area where water will tend to collect, should be repaired as soon as possible. Before sealing the hole, evacuate any water from the hole. Use of a vacuum to extract water is a good method. Use of moderately warm air from a hair dryer or similar heat gun is also a good method to promote water evaporation. Monitor the water in the hole for several days, as water may flow back into the hole from adjacent areas in the hull. It is not unusual for water to be present in some holes for days and days, as it will flow via gravity into the hole areas if its is in a low spot.
Any hole in the exterior of the hull and particularly any hole below the water line should be very carefully inspected and repaired as soon as possible.