You can change terrain height while in the editor at anytime.  It should be under level settings in the lower left menu.  Of course you probably want to change it early before you do much work.

I can't answer the layers question.

I use water planes a lot.  The only real trick you need to know is that you must lightmap them like an object to make them look like water.  Other than that.  Look around in both FH2 and BF2 to find different sizes and shapes.  Joining two water planes or a water plane with the sea can be tricky.  You make have to resort to things like rock dams to hide the gap in level.

No,
There is a "generate atlas lightmaps" option under compile/lightmaps.  It gives you some choice about size and dxt compression(I use default), then it asks to look for obsolete lightmaps.    If you didn't do that, you don't have it.  Those atlas images are the only ones that get packed into the map.  The individuals ones are just used by the editor.

At some point you need to start getting familiar with the files and checking that the editor did the right thing and that the packing script worked as well.  The editor is notorious for screwing up and not saving correctly, etc.

~edit:  I checked your map in game.  Most everything is lightmapped.  I see a few missing on buildings I've never seen before.  You probably don't have the samples for those or for some reason they didn't get added to the atlas.  At this point you can try to fix that and lightmap them idividually, then "generate atlas lightmaps" when done.  You don't have to lightmap everything again.  I'm not sure what problem you are having with the nebelwerfer.  Those player controlled objects don't take lightmaps or leave affect the lightmaps of other things.  They have dynamic shadows in game.  It should break a lightmap but wont help make one either.   Otherwise it's looking pretty good.  You can fix those missing lightmaps later.

If you don't see any lightmaps in gmae, it's because your graphics settings are too low.

You need to generate a lightmap atlas.  That's what the game uses, not the individual lightmap object files.

The 64, 32, and 16 you see in the menu is from the .desc file in the info folder.  You have to edit that.  Just delete the lines that refer to them.  Maybe there is a way to do that in the editor.  I am not sure.

This is a map project.  I don't think he has the ability to make new buildings or new Tigers

I wouldn't worry too much about the gameplay and loadout stuff too much right now.  Just get your map looking good.  That stuff is pretty easy to change when the time comes.
I don't know if you have figured it out yet, but there is no way the FH2 Devs are going to take and release your map in the official mod, so you should consider what will become of it.  Your only real hope is to get it released by the custom community.  It may end up in a tournament.  It might end up getting nav-meshed for single player.  And it might end up released as a pubby map in the CMP map pack.  In each case, you would have different set up and gameplay concerns.  BTW, the current Pacific maps with ships in the CMP don't have spawn-in wrench kits.  This is to avoid ship repair exploit.  Players complain in all-chat but they are certainly used to not being able to repair everything.

Go to the website https://cmp-gaming.com/ and join their Discord or just post on the website.  I'll talk to them about adding you to the Dev team.