I’m not sure what you mean by the problem of putting the maps online because you mention the issue of finding suitable pieces, which implies a board game rather than an online game. I think developing your game as a board game is the best option: it avoids any scanning problems, and I think it’s more satisfying to move pieces on a board rather than electrons on a screen.
If you go the board game route, your best bet would be to use the existing board from an existing Civil War board game – of which there are probably tons on the market. That would save you the work of creating your own board from scratch. You could even use combinations of boards from different games: for instance a board showing the U.S. as a whole (which would serve as your overall situation board for the Civil War), combined with a board showing the world as a whole (to allow you to track the overseas elements, such as the British and French involvement). The world board would ideally be for the mid-19th century, but there may not be many wargames that are global in scale while being set in that time-period, so perhaps using a global Napoleonic-era wargame (I assume there must be some on the market) would be a good compromise for the British/French side of things.
Getting waterline wargaming models of Civil War ships is no problem:
http://www.panzerschiffe.com/Warships_from_the_American_Civil_War.html
There must also be lots of companies that sell Civil War plastic units in all kinds of scales. Ditto for Napoleonic pieces, which could serve as your British and French units. One game that comes with generic pieces that have a Napoleonic flavour is:
http://www.viktorygame.com/.
[Edit: Here’s another source for ships: http://navwar.co.uk/nav/ . Look on pages 6 and 8 of their PDF catalogue (http://navwar.co.uk/nav/pdf/webcat.pdf): they sell 1:3000 scale models of La Gloire and Warrior.]