Hi there! It's not a bother at all. I made this guide to give a hand to others and I try to help in any way I can even though I'm not expert at all.
You said it works in a new game. That's good news, at least there is no bigger problem that keeps it from working. Do you get the MCM menu when you activate it in your existing game? If not, have you tried Jaxonz MCM Kicker?
Do you have a lot of mods or heavy mods in your game, per example Sand of Time or Frostfall? If the Kicker doesn't do the trick, one possible way is to temporarily uninstall and deactivate some of those mods to give the game resources to activate the Command Dragon mod. It is a little risky, as for a short moment your save depends on the scripts that are no longer there, so back up your saves before trying. Or, if the mods you use can be turned off without uninstalling from MCM, it can be safer and quicker way to free some resources for the new mod.
Also, after a little digging, I found that you can try to enter this to console:
setstage Dragonmount_Rong 255
I have not myself tried it but it was suggested by the author themselves as possible solution for problems with the mod so it can be good idea to give it a try.
Welp, I tried the MCM kicker, disabling mods, and the like. It's seemingly becoming more apparent that I have to start a new game.