Hi Renato,
From most photo sources of that point in time, the Akagi, was rather clean at the time of Pearl Harbor. This was, after all, a period when the IJN could still maintain a level of "spit and polish" to their ships since the war wasn't hammering away on them yet.
There was a little weathering simply from the length of the mission, but nothing that would really scream out in 1/350. If anything, the deck would have been spotless.
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How was the overall condition of the ship??
Excellent
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Was she kept in good condition?
As the ship that Yamamoto had a particular soft spot in his heart for (and carrier force flagship), most definitely.
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Was there alot of "touch up" paint?
At that point, probably not, but that's because the ship's stanadrd paint job would have been clean.
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Would there be alot of salt stains?
Some, due the length of the mission, but again, nothing that would probably scream out in 1/350 due to the scale effect.
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Did she show rust stains on her hull? along railings and chains?
At this point time, no. Midway, there would have been some. In fact, by Midway, the Akagi had done much more in wartime (Port Darwin Raid, Indian Ocean, etc.), and thus would enhance weathering possibilities.
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Did her linoleum show wear or sunbleaching??
Again, at this point, no. Of course, you can always take artistic license with anything, but in real life, she was clean.
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Did she have any damage prior to Pearl?
No. She was rebuilt to her single deck configuration in 1938 and nothing fateful happened between then and Pearl.
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Did her flight deck show alot of oil stains? landing marks? wear and uv exposure? and grime?
No. At this point, the pride of the Kido Butai was spotless, as a flagship should be.
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The Carrier Planes
Were they in good conditon? Or battle worn?
Did suffer from the elements aswell? or kept clean and well maintained??
The planes were all in good condition and well maintained. Again, you can choose to use some artistic license, but in real life, those planes were kept in perfect condition (paint supplies hadn't run out or degraded in quality yet).
For more info on the Akagi's movements, check out the always helpful Combined Fleet.
http://www.combinedfleet.com/Akagi.htm All in all, you'll probably use some washes to bring out details, but as for long, wild rust stains, etc., none of those would have been present on her in any large degree for the attack on Pearl.