connectors? I think I see an IDE connector in the one pic.
If you have IDE connectors, you can get CF -> IDE adapters, then you could go more than 4GB for a disk. And I believe you could then do NTFS as well.
And I do not know enough help you with the install issue.
Or you could just get a bunch of small SSDs and hook them to the IDE. SSDs these days have a pretty decent long life. I am using one in the car.