Well, I THINK have them figured out now, but it has taken me several hours for 2 friggen holes... LOL
To have a great search-able post, I'll work through the steps here. Make any corrections or suggestions and I'll edit this OP.
1) Help me Obi-Wan Kenobi, you're my only hope... Open PcbNew, and depress the "o" key (( or left click the "Add Component" button) (or find it in the menu bar)), then click the location on the board where you want a mounting hole. A new window will pop-up, and I recommend choosing the "Select by Browser" method.
1a) Once the above button is clicked, navigate to the "Mounting_Holes" library in the left pane and left click on it. There are a lot of choices, but none of them were exactly right for my needs. It was easiest to just pick one at random (to edit after placement); left double click on one of them!
1b) Despite being required to click a location first, it is required to left click again to confirm that is where you wanted to place it.
HINT/NOTE: It LOOKS like a single pad, it really is not. It is a component without a body. It is needed to select the component for the next step.
2) Select the mounting hole component (recommend by left-clicking on the outside of the visual edge and "clarifying" the selection) the and depress the "e" key (or right click on:
2a) Legacy canvas: "Edit Parameters"
or: OpenGL canvas: "Properties"
Note: It really is simpler to just depress the "e" key.
3) You're Going to Need a Bigger Boat... Notice that in the "Move and Place" section, the "Lock Pads" option is selected. Change that selection to "Free"; then click "OK".
4) Left click in the center of the component (on the pad itself) and depress the "e" key or ^^^ select as shown above ^^^.
5) In the "Pad Type" drop down menu, select "NPTH, Mechanical".
5a)Edit the pad dimensions to your requirements.
HINT/NOTE: The number on the pad is no longer visible, but it is still a component.
6) Toto, I've a feeling we're not in Kansas anymore. Using OpenGL Canvas) Left click on the center of the pad/component and depress "Ctrl" + "e".
6a)Edit the pad dimensions to your requirements.
HINT/NOTE: Since, even now it remains a component; even though we just want a hole, I recommend changing the "Ref**" text, and the "MountingHole..." text (on the fab layer) to invisible.
HINT/NOTE: KiCad itself knows that this text is there. The Gethub library names are very long. I recommend changing the name to just "hole" and later moving the hidden text INSIDE the board edges. If you are curious as to why, leave the long name way outside the board edges. After finishing step 9) in this post, then depress the "Home" key to find out.
7) Left click, on the top menu bar, the "Update footprint in current board". Close the editor.
8)Select the mounting hole component (recommend by left-clicking on the outside of the visual edge and "clarifying" the selection) the and depress the "e" key or ^^^ select as shown above ^^^.
9) Notice that in the "Move and Place" section, the "Free" option is selected. Change that selection to "Lock footprint"; then click "OK".
HINT/NOTE: In the Netlist importer, There is an option to Keep or Delete Single Pad Nets. Well, I usually check Delete for all the selections. Guess what "Single Pad Nets" actually means and how I figured it out when my holes all vanished every time I re-read the Netlist. I know that locking the footprint keeps the Netlist reader from making the PCB holes vanish. Select, or test, locking only the "pad" at your own peril.
10) Hey Steve, did ya bring me any pizza Steve? Duplicate the hole as many times as needed.