Hi Rick,
I've made a lot of progress converting my small WWHB project over to DM, and am working my way through the build and deploy workflow. For some context, I've been using WWHB's process to generate HTML and save to a zip file. I then use my zip client to unpack to the various websites where I host my help content (dev/stage/production).
This same approach works with DM but I'm wondering about the pros and cons of the myriad alternatives for publishing.
Some pictures with their associated 1000 words...
I also tried the FTP route.
Here's the log that got generated at the end of the FTP process.
Publish errors to ftp.rfcsystems.com
Code: 550 Message: File Blue not found
C:\Users\rkaye\Documents\rfc3docs\rfc3 apis\wwwroot\_docmonster\themes\Blue Lagoon\classconstructor.html
Code: 550 Message: File Blue not found
C:\Users\rkaye\Documents\rfc3docs\rfc3 apis\wwwroot\_docmonster\themes\Blue Lagoon\classevent.html
Code: 550 Message: File Blue not found
C:\Users\rkaye\Documents\rfc3docs\rfc3 apis\wwwroot\_docmonster\themes\Blue Lagoon\classfield.html
Code: 550 Message: File Blue not found
C:\Users\rkaye\Documents\rfc3docs\rfc3 apis\wwwroot\_docmonster\themes\Blue Lagoon\classheader.html
Code: 550 Message: File Blue not found
C:\Users\rkaye\Documents\rfc3docs\rfc3 apis\wwwroot\_docmonster\themes\Blue Lagoon\classmethod.html
Code: 550 Message: File Blue not found
C:\Users\rkaye\Documents\rfc3docs\rfc3 apis\wwwroot\_docmonster\themes\Blue Lagoon\classproperty.html
Code: 550 Message: File Blue not found
C:\Users\rkaye\Documents\rfc3docs\rfc3 apis\wwwroot\_docmonster\themes\Blue Lagoon\database.html
Code: 550 Message: File Blue not found
C:\Users\rkaye\Documents\rfc3docs\rfc3 apis\wwwroot\_docmonster\themes\Blue Lagoon\datacolumn.html
Code: 550 Message: File Blue not found
C:\Users\rkaye\Documents\rfc3docs\rfc3 apis\wwwroot\_docmonster\themes\Blue Lagoon\datastoredproc.html
Code: 550 Message: File Blue not found
C:\Users\rkaye\Documents\rfc3docs\rfc3 apis\wwwroot\_docmonster\themes\Blue Lagoon\datatable.html
Code: 550 Message: File Blue not found
C:\Users\rkaye\Documents\rfc3docs\rfc3 apis\wwwroot\_docmonster\themes\Blue Lagoon\dataview.html
Code: 550 Message: File Blue not found
C:\Users\rkaye\Documents\rfc3docs\rfc3 apis\wwwroot\_docmonster\themes\Blue Lagoon\delegate.html
Code: 550 Message: File Blue not found
C:\Users\rkaye\Documents\rfc3docs\rfc3 apis\wwwroot\_docmonster\themes\Blue Lagoon\docmonster-dark.css
Code: 550 Message: File Blue not found
C:\Users\rkaye\Documents\rfc3docs\rfc3 apis\wwwroot\_docmonster\themes\Blue Lagoon\docmonster.css
Code: 550 Message: File Blue not found
C:\Users\rkaye\Documents\rfc3docs\rfc3 apis\wwwroot\_docmonster\themes\Blue Lagoon\enum.html
Code: 550 Message: File Blue not found
C:\Users\rkaye\Documents\rfc3docs\rfc3 apis\wwwroot\_docmonster\themes\Blue Lagoon\header.html
Code: 550 Message: File Blue not found
C:\Users\rkaye\Documents\rfc3docs\rfc3 apis\wwwroot\_docmonster\themes\Blue Lagoon\index.html
Code: 550 Message: File Blue not found
C:\Users\rkaye\Documents\rfc3docs\rfc3 apis\wwwroot\_docmonster\themes\Blue Lagoon\interface.html
Code: 550 Message: File Blue not found
C:\Users\rkaye\Documents\rfc3docs\rfc3 apis\wwwroot\_docmonster\themes\Blue Lagoon\namespace.html
Code: 550 Message: File Blue not found
C:\Users\rkaye\Documents\rfc3docs\rfc3 apis\wwwroot\_docmonster\themes\Blue Lagoon\notopic.html
Code: 550 Message: File Blue not found
C:\Users\rkaye\Documents\rfc3docs\rfc3 apis\wwwroot\_docmonster\themes\Blue Lagoon\struct.html
Code: 550 Message: File Blue not found
C:\Users\rkaye\Documents\rfc3docs\rfc3 apis\wwwroot\_docmonster\themes\Blue Lagoon\tableofcontents.html
Code: 550 Message: File Blue not found
C:\Users\rkaye\Documents\rfc3docs\rfc3 apis\wwwroot\_docmonster\themes\Blue Lagoon\topic.html
Code: 550 Message: File Blue not found
C:\Users\rkaye\Documents\rfc3docs\rfc3 apis\wwwroot\_docmonster\themes\Blue Lagoon\Under-Construction-Partial.html
Code: 550 Message: File Blue not found
C:\Users\rkaye\Documents\rfc3docs\rfc3 apis\wwwroot\_docmonster\themes\Blue Lagoon\weblink.html
Code: 550 Message: File Blue not found
C:\Users\rkaye\Documents\rfc3docs\rfc3 apis\wwwroot\_docmonster\themes\Blue Lagoon\webservice.html
Code: 550 Message: File Blue not found
C:\Users\rkaye\Documents\rfc3docs\rfc3 apis\wwwroot\_docmonster\themes\Blue Lagoon\webserviceendpoint.html
Code: 550 Message: File Blue not found
C:\Users\rkaye\Documents\rfc3docs\rfc3 apis\wwwroot\_docmonster\themes\Blue Lagoon\whatsnew.html
Code: 550 Message: File Blue not found
C:\Users\rkaye\Documents\rfc3docs\rfc3 apis\wwwroot\_docmonster\themes\Blue Lagoon\_layout.html
Code: 550 Message: File rfc3 not found
C:\Users\rkaye\Documents\rfc3docs\rfc3 apis\wwwroot\rfc3 apis.docs.json
Note that I was just uploading to a test folder in my FTP server and not actually pushing the files to their final destination. For that to work I'll need to setup virtual folders in my FTP environment that point at the proper destinations.
At the risk of stating the obvious, all 3 paths I tried are including the extraneous files highlighted in the 2nd screenshot.
All in all it's looking very promising and I'm confident this will be an excellent migration path out of WWHB.

You need to break these up into separate issues. On GitHub or here. Otherwise this is a mess to respond to.
+++ Rick ---
Will do. Do you have a preference between here or GH issues/comments?