So, here is the current state of affairs:
I spent the day walking back my decision to use nails for the scarf joints. First, I removed the blackened nails with a utility knife blade. Several flesh wounds later I carefully cleaned off the stained wood using a barely damp cloth - this removed about half the staining. Next, I spot sanded the joints in an attempt to remove the more stubborn stains - this helped a bit but not as much as I was hoping. My reward was I got to clean out scarf joints again... Next, I rubbed down the lower half of the hull with a rag using the bare minimum of linseed oil. I then tinted the holes with an archival ink pen.
First, a view of the hull as it exists after a day of remedial work...
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Here's a closer look:
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And this:
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The nail representations are not as precise as I created around the gun ports but I think I am moving in the right direction. While it may not be as evident in the photos - the over-the-top visual impact of the nails has been greatly contained. I can work with this.
I do intend to use actual nails on the wales - smaller ones at the scarf joints and some larger ones along the length.
What I have not figured out is how to now add frame nails to the hull. Brass wire without a nail head? Try my tiny brass nails again (but blackened ahead of time!)? Is there a place for treenails?
As I mentioned previously I am not envisioning a hull that is more about nails and nailing patterns than it is about wood. I acknowledge that there are some majestic Vasa builds that chose to go in the direction of a nail-dense hull - but I have a different goal in mind. The picture I posted of the stern of my ship is pretty close to the look I'm going for...
In the mean time, I'm going to "slow my roll" and revisit some of the Vasa build logs I know about - and also follow-up on the builds
@Mr.Deep pointed me to (as well as others I might be able to find on some of the international forums). I'm looking for inspiration and technique.
Of course, I still need to remove the brass nails on the other side of the ship. Since that side was never blackened there will be less cleaning and sanding, but just as many flesh wounds...
SO MANY LESSONS LEARNED!!! Thanks everyone! You're a fine bunch!