1) In a custom install you can decide what part you install. For Sense in a 1 server environment you simply take the Full install. In a multi node environment, you will do a Custom install for all your servers past the 1st so to decide what kind of RIM node you are running.
2) Without the repository your server is useless. This thing keeps track of most of the settings, all security rules, etc. You will need a repository on every server in your environment. Sync. rules will be setup to keep them nicely in sync.
3) Been too long since I did an install; I fear I can't help you with that one.
Don't allow Perfection to be the enemy of Good Enough. May you live in interesting times!