1. Yeah, personally, just get the Digital I/O. Here's a great comparison -->
viewtopic.php?p=7186#p7186 -- As you can see, the VGA out, SoG Switch are just for CRT's (and you can use a Direct Video HDMI to VGA adapter to do CRT's regardless if you ever change your mind), so the only thing is the 3.5mm headphone jack out, which personally... is a bit noisy from EMI on the board, and it's a combo Mini-Toslink regardless so I just used TOSLINK when I used to have my Analog board, and would use a DAC to convert to analog audio externally when I used it with a CRT.
2. USB HDD is... sometimes confusing for people. I have tried it a long time ago, one time I got it going, and the instructions that were available at the time were not totally clear on some of the specific things you have to do. Now I understand it's a bit easier and the guides are better. I'm pretty sure SmokeMonster's guide is still relevant -->
https://www.youtube.com/watch?v=vqRKaBt_Oq8
3. There are plenty of places to buy cases, yes!
https://www.etsy.com/listing/789104565/ ... decal-pack - (My personal favorite to recommend if you are waiting on a nicer case, since it's cheap and easy).
There are plenty of other places too. The main thing to keep in mind with the MiSTer is always statically discharge yourself before touching it. This also includes when you DO get a case btw. The metal case from MiSTerAddons can absolutely get static shocked and pass that static into the device. Same with Acrylic and other materials. I usually just touch something metal for quite some time before I touch the MiSTer. I have to do this a lot since Colorado is super dry. When touching PCB's, pick up by the sides, not underneath.