I would start small and purchase an 8086 embedded development kit, and develop a multitasking OS on that. Once you have a kernel and are acquainted with working at the hardware level, you will be ready to do something more challenging.
Building even a VGA display DOS clone is a fairly challenging thing. The details are enormous. :-)
specific topics.
How do I put the code onto the computer? Is it best to do it with a floppy disk? Can most computers do it from a USB stick?
The BIOS will do elementary bootstrapping.
What drivers do I need, and can you suggest any references to building those?
anything that isn't direct cpu/memory operations. Anything that isn't directly in the CPU reference manual.
After the booting sequence--then what? How do I get into protected mode etc.
Protected mode will be part of the boot sequence.
then you start multitasking and figuring out how to start processes.
How do I manage memory without the help of an operating system? Do I just use whatever addresses I want? No initialization necessary?
Correct. You will probably want to sort out a virtual memory system eventually.
What will I undoubtedly run into that will confuse me?
not having debugging tools, not having IO
How can I make it either a command line O/S, and a graphical one?
With grief. Look up Windows 3.1 and Linux, in particular X windows.
What is a graphical O/S built on? Like, how would I do something like, a command line, with a font, and a picture at the top?
Look up X windows.
final advice: study linux/x windows. It's not perfect, but it provides an understanding of one approach. Also study embedded systems.