Some A's to your Q's: (if I'm wrong, someone else jump in and correct it).
1 - Yes, your device with a bootloader (either it's USB or CF) is needed every time you boot the computer, so leave it in.
2 - Yes, each drive will have at least 3 partitions: System, Swap, and Data, the first 2 are identical on all the drives.
3 - The new bootloader will see your current config, and let you know that you have "Moved your disks from a 3612xs to a 3615xs" and tell you that you can do a migration.
You can select to only migrate your data, and reset all setting, or migrate all.
4 - The tricky one ... not sure if your controller managed array will work this way, as the most common way to do this with DSM is to let the OS (if it has the drivers) do the raid work.
Before you do anyting, make sure you have backup of all important files.