No offense meant, but you asking these questions (esp. 1) kind of leaves me in doubt that you're really up to the task...
If you don't target the Amiga as primary system, but just use it as a development platform, there's no need for 2) since you leave it to normal Kickstart to setup the hardware (RAM, caches, IDE, video, ...) and then take over the machine much like most games do it or other OSes.
If you're going to ask 'Then how do I take over the machine?' you're definitely not up to it, sorry.
Furthermore, writing a modern OS is nothing one single person can do in his lifetime...
