If you relocate the slow RAM make sure you cut _EXRAM as well (otherwise the RAM will appear in two different locations and the system will crash). The 2 MB chip RAM expansion requires this mod as well.
2. The Gary chip lines are for providing the extra addressing required. The Agnus socket as is can only address 1 MB.
3. Agnus pinouts can be found in the service manuals. I've added a comparison chart to
Wikipedia a while ago. The inner workings are not so easy, there are several somewhat complex state engines. You should take a look at the Hardware Reference Manuals.
4. Yes, Agnus is doing chip/slow RAM refresh as well.