You are welcome to ask specific questions about each of those issues.
File Options can auto-enter an account name and password while you can hold down the shift key to force a password dialog to open so that you can enter credentials for full access. There's a script step that can install specific custom menus and other script steps can hide and lock the status area tool bar if you want that.
Window sizes can be specified in the New Window command, and if the layout is in for view, there's also Adjust Window [Resize to fit] that can be used to get the window to automatically "fit" the window to the layout. And there advanced window options you can select for a new window script command that can ensure that the window floats and/or functions as a "modal" dialog.
PS. In FileMaker 13 I am using new window to produce modal dialogs much less often than before. I use a popover for the same purspose and it takes much less effort to set up.