There is a bug with a few of the Cos3 templates. You can grab an updated version of the installer from your reg page, or download the fixed templates only from here. That should hopefully fix things for you (note that fixed templates means it will work properly on new maps crated from these. For existing maps, I recommend just copying things over to a new map once you have confirmed this fix works for you)

Your map is 250 by 200 feet, so that is 50 by 40 squares. Each square in FG is 50 pixels by default, so should be 2500 by 2000 pixel export if my calculations are right

First, load and apply the Mars color setting

Then, go to the Altitude tab of the Lighting and Color dialog, here you can set blue colors for the sea. Just set the sea level and lowest depth color, FT3 will calculate those in between, and you'll probably want to bump up the value for number of colors too.

Not easily unfortunately. Would have to figure out how the plugin that provides that functionality works and rewrite parts of it.

They are, it's just less noticeable because they are broken up into individual letters.