The maps only work in cities or newbie zones. Once you venture forth beyond those safe areas, you won't have a map and will be glad for max sense-heading. This is a client issue and it's not really possible to disable them. That said, if you want, you can always delete all the .txt files in your Maps folder
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the UI has a variety of settings for transparency and when to fade in and out of being transparent. You may have to use the right-click menu on each window and set it's transparency settings individually. I can't remember for sure.
As others have stated, working boats are pretty much impossible. The reason for this is that we're using a post-DirectX9 client, and even Verant/SOE admitted that old-school boats can't work with this client and replaced them all with translocators. The only EMU I know of with working boats is Shards of Dalya, but that is because they use a much older (pre-DirectX9) client.
That said, the devs have done a good job with the translocators, by having them spawn and despawn on a schedule that matches when the boats used to come to the docks back in 1999 on live. So although you don't get to enjoy the ride on a boat itself, inter-continental travel is still fairly slow and arduous without finding a player to port you. This is one case where the 'spirit' of 1999 is kept alive, even if the actual details are different.