Daniel,
The linseed treatment (or any oil) will always bring out variations in the planking. Timber is not uniform, and in fact if you look at the actual Vasa, you will notice this variation too (although its a little hard to see in the light of the museum - I don't seem to have a good photo of the deck planking).
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What have you used for the planking edges? You seem to have good 'tarring' between the planking, and it is quite uniform.
I also note that you have removed the tops of your bulkheads for the midships where they protrude through the decking. Was this to get them to fit, or was it that they were just to weakened when sanded. I had the same issue and just replaced them as the side planking came up around the ship and the upper decking.
Your gratings look excellent and I know its a lot of work, but it really enhances the appearance. Have you finished these for colour/stain or will they be darkened?
Great progress.
PeterG