Hi Aaron.
3 months in a container is not ideal, but survivable. Humidity and temperature swings will be buffered by sealed packaging as mentioned. I'd also make sure the ends of the timber pieces themselves are sealed first and that your sets are nice and tightly bundled together flat, potentially between two thicker outer packers so they don't warp around. Make sure there are no bark or similar inclusions on the timber too. It might also help if you tape a list of what is packaged within, to the box itself. That is, quantities and species and intended use (eg 1 x Blackwood (Acacia melanoxylon) guitar set from Australia). Likely unnecessary, but it may help should customs inspect it on entry to your destination.
I've not shipped any timber by container, but when shipping internationally by air, you need to fill in a customs declaration form yourself. Likely your work has a broker doing that for the container and they may ask you about the contents in detail. Check they are insuring it for you.
When filling in the customs declaration, you have to enter the tariff numbers for each item, quantities etc. You can look these up online, but prepare to get confused!! They are full of particulars you have to work out such as - over 6mm thick; under 6mm thick; rough sawn unprocessed boards; dressed boards/products; right down to genus sub-categories within each etc. Species and country of origin is also required. I had to do all this for every shipment of timber that left the country.
Chances are it will all go through without a hitch either way, but it won't hurt to be as prepared as you can. That way, you've done everything reasonable to ensure it does.
Hope that helps.
Cheers,
Jeremy.
