Issue #1: I won't have access to the server on which my updates will be placed. I'll have to email them to someone who will email them to someone else who will upload them... So; it's the contents of the "Update" folder? And it "overwrites" a previous version?
Yes, it's more or less the contents of the "Updates" folder. You'll also have old files in that folder after you start releasing new versions. So, if you want to ensure only the newest files are sent to whoever uploads them to the server, then delete (or rename) the Updates folder before building the new updates.
Or just sort the files by date and only include the files generated since you clicked the "Build Updates" button.
Issue #2: I'm only allowed to place ZIP files on the server... So I can change the extension of the files to be .ZIP to be allowable? (I will own up to the server admin that they're not actually ZIP; just a binary file) {I think there will be 3 files? the info file, the patch file and a whole app install file for first time users?}
You can rename the files to have a zip extension. In wyBuild go to File -> Properties -> Update and server files and then edit the ".wyu" and ".wys" extensions to be ".zip".
Issue #3: I can't guarantee that the users of this program will have unfettered web access; they may be restricted to the intranet (and the server with these files on)... So I'll need to do my own version of wyUpdate.EXE? That'll make it 4 or more files in total?
Well, there are a few things you can do. You won't need to make your own version of wyUpdate, but you might have to host self-updates to wyUpdate on your own server. See: How to make a custom version of wyUpdate. You can ignore the parts about compiling your own version of wyUpdate. Just use our pre-compiled version.
Tell me if this helps.