Since nobody else wants to start, I guess I will.
#1, you already seem to understand that you need to develop new habits. Play with workspaces, setting up panels you'll find useful, and save the workspace. I haven't used Quark since version 6, but I find the interface far more productive in ID than I ever did in Quark.
#2. master pages in ID are a very different concept than they are in Quark. You can override master objects, but if you do you ought to be thinking twice about why you put them on the master page to begin with. I'd say about 90% of the time if you are overriding it probably shouldn't be on the master at all. To override a single object, press Cmd + Shift and click (Mac) or Ctrl + Shift and click (PC).
You don't need to override master frames to Place (the equivalent of Get Text or Get Picture) content into them. Just click inside the frame area and ID will override automatically, and if yo are flowing text you shouldn't override manually because doing so will disconnect that frame from the master thread. But even better, you don't need a preexisting frame at all to place content. ID will draw a frame for you on the fly. In my work I seldom use master text frames -- they're actually more often a hindrance than a help unless you have odd layouts that don't use frames snapped to the margin or column guides. And I personally don't use Smart Text Reflow, though you might like it as it works similarly to Quarks automatic frame additions as you overfill a page when you type.
"In my ID document, I see the text frame that came from the Master Page, but it sits behind a text frame that’s actually being used for my body text! Is this because of how my document came in from Quark?" More than likely. Master frames get reapplied if you change the master, or if your page swaps sides on a spread, or maybe it just didn't get used. In any event, Master page objects are behind all live document page objects on any given layer, so you may need multiple layers if you have, for example, content like an automatic page number on the master page that needs to appear in front of an image on the document page.
#3, Shuffling should be enabled by default. It just means that if you move pages, the others bump position. You would disable shuffling when you want to add a page to an existing spread to make a foldout, or something similar (or to build a multi-page spread from non-facing pages for a three-fold brochure). The default panel view is similar to Quark's vertical layout, but it's much more efficient to show the pages horizontally in the panel.
There are some books, I think, targeted to transitioning Quark users over to ID, but you should really also check out Sandee Cohen's Visual QuickStart Guide to InDesign, and Real World InDesign by David Blatner et al. The first is a great beginners book, and the second is the "bible" for more advanced users and presents topics in plain language and explains the why as well as the how for making the most of the program in the real world.
Peter has answered your specific questions very well. But I don't know how advanced a "Quarker" you were (are). But here are a few of the "gotchas" that may snag you.
Leading: Leading in XP is a paragraph attribute. Change the leading on one line and the whole paragraph adjusts. Leading is a character attribute in ID. So you can have lines within a paragraph with unequal leading. If this bugs you (and it does many people) change it in Preferences > Type > Apply Leading to Entire Paragraphs
Text Wrap (Runaround): In XP runaround only works downward. So anything above the text frame won't be affected. ID text wrap works both up and down. Again, go to Preferences > Composition > Text Wrap Only Affects Text Beneath. There are some times when you don't want this turned on, but that's a more esoteric topic.
Tracking and Kerning: InDesign uses smaller units than XP. So if you usually track at -2, you should multiply that amount by 5 to get the equivalent in ID. Same for kerning.
Frame contents: Even though they are labeled as text frames, graphic frames, and unassigned frames, you can put anything in each one. Select a graphic frame (the one with the X in it) and you can choose to Place text. Select an unassigned frame and you can place an image. It's wacky, I know, but very helpful.
Character Styles: I hope you used text styles in XP, if not you should start now. However, Character Styles work differently than XP. Define the Paragraph Style with ALL the character attributes. Font, point size, tracking, color, etc. Then, if you want the text to be italic, create a character style that is only that one attribute—italicness. You don't have to specify font, point size, etc. That way one character style can be used for several different Paragraphs.
There's lots more, but if you tell us a little about the kind of work you do, we can make more suggestions.
And yes, I do recommend my book. But I also recommend coming here for help.
Peter and Sandee,
Thank you BOTH for taking the time to give some thorough responses to my post.
The information is most helpful to me and clued me into some things I might not have been aware of.
I now have a better sense of how I might use (or not !) text frames in Master Pages. I'm also clearer now on what is meant by page "shuffling".
Thank you also for pointing out the information about Tracking and Kerning, as well about Character Styles, and the leads to the book resources available.
I will eventually play around with ID more to get more hands-on knowledge.
I use Quark for professional-looking business documents as well as for creative writing, because how words appear visually on a page is part of the experience for me. My most ambitious Quark project was a book that combined my own research, creative prose, and photographs, so there were different sections (intro, body, end notes, list of works cited, etc) and consistent styles that carried through the book. It was a challenge to find a way to harmonize the placement of images along with the flow of text. I don't really consider myself a designer, but I appreciate considered relationships between elements on a page!
Regards, and best to you both!