It's always okay to bump something after a month has passed.
Yes, direct fire = terrain mods apply. Indirect is just better in this case (though note that the TAGging unit had to worry about terrain mods to nail the TAG in the first place, so it's not like the terrain didn't have some effect).
As for partial cover provided by water, indirect fire already has a note stating that you ignore the TN mod it provides, but leg protection still applies, so we're going with that for consistency's sake. However, there will be a bit of errata added to the BMM to make that crystal clear.