In general I agree with what you did, but I also agree with orthocresol's comment. At the current size of the catalogue it is probably a good idea to run it past meta first, get one or two opinions and make the rest of us aware that there might be some retagging going on. (You can of course always also find advice in chat.)
Next I'd like to point to the help center about tagging. (If I can remember or find the "other" resource about tag deletion etc., I'll edit it here.)
That all being said, let's get to your questions:
- Could someone with the magical power please fix the tag spelling?
Or tell me what I need to do to fix this?
In principle, you already can, see below. The question becomes whether you should, but I'll also explain that below.
- I'm thinking that if I had replaced all the Van-der-Waals-behavor tags with Van-der-Waals-behavior tags that then both would stay in the system even though no questions were tagged with Van-der-Waals-behavor.
That is a little bit correct and a little bit wrong. Abandoned tags will get cleared/purged from the system (iirc) around midnight-ish UTC. If you immediately change it when you notice the tag is missspelt, it might linger around. Sure, there could be occasions when an innocent user comes along and applies it again, but these are rather slimmish.
That's the procedure which is most common and I would recommend it for everything fewer than 5 (at most 10) edits. There is still one point to consider before doing it, I'll get to that below.
- When editing the tag information I got befuddled by the direction to use no markup. In retrospect it would seem to only apply to the top section which gives the "floating text" rather than the bottom section which gives the detailed explanation.
The tag wiki excerpt, this is the blurb you see when you hover over a tag, must be plain text. This should contain information to the usage of it.
The longer tag wiki entry can be the usual markdown. It should also include a little bit on usage, but some background info and resources, maybe co-tags, but that's entirely up to you. You can also leave it blank.
The tag wiki excerpt is more important, as it gives us (and the new) users a better idea when to apply it, especially when there are only a few questions yet tagged with it.
Special case: When you've went through all the trouble of creating the wiki entry, it might be a good idea to keep it alive. Still given there's a few uses only, you can manually copy it over, or contact the mods, again see below.
Is there a way to flag a tag for deletion?
I didn't mind doing the work to fix the four question with the misspelled tag, but I didn't want to leave a junk tag in the system which would cause confusion.
See above (recursive cross reference ;p). Like I said, abandoned tags will be deleted, so there is no need to flag. The mods wouldn't do anything else than what you would do.
What else to consider? When should I flag?
Moderators can merge tags, they can rename tags, and they have access to abandoned tag wikis. For example, if we would like to change homework to homework-ish, we can do it for the (currently) 700+ cases in one go. That comes in handy because it doesn't flush the front page (multiple times). So consider that for 10+ edits. Simply flag one of the questions with the tag, or open a meta post to discuss it first.
If a tag wiki gets lost in editing, we might be able to retrieve it. I don't know exactly how it works with renaming, and whether or not the wiki will be kept, but we can find that out when needed.
If you are unsure, ask. Here is a good place. If you're lucky you might find someone in chat who already knows the answer, too.