So, a series of things were happening, and I've got it working now, but not sure how/why.
I made my son an Administrator (ugh), then I had to open all permissions to every account on the computer. This was a huge ordeal involving the RUN program, CMD, a command line prompt, and some clever creation of a new ghost "Hidden" administrator account..... This didn't fix the issue.
I then found an issue with the "Ownership" of the file... somehow we didn't "own" the file (for some reason). I tried re-downloading it, so I could "own" it.... didn't help for some reason.
I then tried a workaround whereby I moved the program folder to another directory and renamed it to something completely different (in this case "Chickentown") and then restarted the computer, booting back up in Safe Mode. In Safe Mode, I moved the folder back into the desired directory, changing the name back to Classic99.
Once this was done, i tried to run it. Our antivirus stopped it, letting me know that the program would blow up my house, violate my cats, and piss on my face. I had to manually force the AV to allow Classic99.... then re-start to "accept the changes."
Once back in, I launched Classic99 and the screen blew up to something like 200% magnification. I dug through and found a setting somewhere in the drop down menus that was forcing Classic99 to run at 640x580 pixels or something like that. I unclicked that box, relaunched, and now it works like a charm.
3 hours later, and I hate Windows 10 so freaking much right now.
Barrage is great... the controls feel pretty good and it really scratches my Missile Command itch when I have it...
But it is NOT Missile command...
As far as the TracBall is concerned, I don't know if it works on all joystick games... I am 100% sure that it wouldn't work CORRECTLY on all joystick games though. I know there are many here more technically gifted than I who can tell you more about it.
Id like to try the TracBall on Parallax Starfield.