All correct with a few minor notes:
Covering the panels is not that important IMHO. If you disconnect the battery side of the charge controller by removing the fuse there will be no load on the charge controller so no current will flow to the controller or beyond. And besides you don't care about that controller anymore anyway.
Yes, it is DIY. Not really tricky if you have some basic wiring skills and can perceive what's happening with the overall system. Yes, go bigger if you plan on replacing/adding more panels later. The 100/50 isn't that much more. For Wonder owners: you don't have room, really, for more than four panels so the 100/30 is fine.
Yes, add circuit breakers per SS between the panels and the charge controller (eliminating the need? to cover the panels) and between the charge controller and the batteries. Make sure they are both turned off. The connection between the charge controller and the batteries obviously provides power to the charge controller so it can boot up and find its mind! After I wire one up I turn on the breaker to the batteries and let the controller boot and then flip the breaker for the panels and watch what happens via the Victron Bluetooth app on my phone. Instant gratification as you watch the amps run off the roof into your batteries!
Tampa mentioned putting the controller in the inverter bay and wiring it to the batteries in the battery bay. Not really necessary, although technically correct. You can wire the charge controller directly to the inverter positive and negative instead. Shorter run and the wiring between the inverter and the batteries is heavy duty. Your choice. I've taken to wiring to the inverter as it's simply simpler!
You might as well add the Victron battery monitor too. Another $200 or so but worth it. In my Unity I had upgraded the Magnum remote to the more functional one but still think the Victron is better. That said, the more functional Magnum will allow you to tweak your converter/charger settings within the Magnum inverter to better support charging your lithium batteries so maybe worth it too.
Echo the concerns about the interaction and incomplete charging by all systems working on the problem. I think the alternator is the weak link as there isn't any way to tweak its behavior. There is a thread in this forum discussing a DC to DC charge controller that is programmable. I think if I were to spend the dough on a lithium system I'd install one of these too. For those of you with lead acid batteries I don't think you need to over worry that. If you're like me, and I know I am, I roll into camp in the mid to late afternoon and the solar completes that last little bit of charging before the sun sets.
One last thing for the OP: when you replace the charge controller you will want to rewire your panels from pure parallel to a series/parallel configuration. You can do that on the roof with the Y connectors. When you do this you raise the voltage coming down to the charge controller from12V (nominal) to 24V. This results in less voltage drop (as far as the system is concerned) and helps to overcome the fact that the wire size from the roof to the battery compartment is not really optimal. Some folks have rewired the panels to the battery/inverter bay. I don't think that's really necessary if you rewire the panels. That said, if you want to create the perfect install that's probably what should be done. But the gain will be nominal and always remember that perfect can be the enemy of good.
I'm toying with the idea of writing (with everyone's help) and comprehensive/consolidated topic covering all of this. We have collected a ton of wisdom on the issue of the perfect solar design/implementation but it is scattered across numerous topics and thus hard to find/read/digest.
And, as always, if you can catch me in Show Low or Rio Verde I'm happy to help you out with this stuff in my driveway!