1) I recommend replacing your custom values value list with a "use values from field" value list. Put your values into a table and add a button or your own "action" value inside the value list for running your own script for adding a new record with a new value to the table. I would recommend this over using custom values with the "edit" option even when not publishing to the web. (See link below for a demonstration file that shows how to put "action values" into a "use values from field" value list.)
2) You can upload to the server again. But you have to close and remove the current hosted copy. It's not clear here why you would want to set sharing options to "no user". This is an automatic feature of FileMaker, but it should not be a significant problem. If you want to use the hosted file, select that option, if you are doing development work on a local copy select the option for the local file.
4) Don't see why this is an issue. Most layouts in a file (you can end up with many layouts in one file, even hundreds) will not have the same name as the original file. Here's what happens: When you first create a new file, FileMaker creates the first table for you and names it after your current file name. It then creates a table occurrence "box" in manage | Database | relationships and a layout based on that table occurrence with exactly the same name. I would give this layout (and the table) a name that is not the same as the file name in the first place.
The WINDOW name will update to match your new file name unless you write a script to renamed it and that should be sufficient to help you identify the current copy of the file that you have open. You can also set up an unstored calculation field or use the Insert menu (other symbols...) to insert layout text on your layout that displays the current file name.