Chronoleon's miniature and her improvement tokens don't populate when she's chosen from the setup menu. That being said it's not a huge issue since I was able to copy and save her miniature when the game first loads up. Great mod!

The way I choose to do the setup is that you choose how many players only in competitive play. When you choose to play solo/coop the player count dosent matter because the setup is the same either way.
Which button is greyed out for you?
Strange about the clockhands... works for me. Which setup did you choose when you have that problem?

Right-click and then left-click doesn't move the clockhand or the master plan track

Thanks for adding co-cop, but if I choose solo/coop, I can't after it select for 2 players in the setup window. It is greyed out.

You can set up the game either in One-vs-Many-mode (OvM) by choosing number of players or
set it up for solo & cooperative mode (S&C) by choosing that.

I don't quite understand the question. I'm under the impression that solo play has the same setup as coop i.e. you play solo or with friends against an automated machine.
Is there anything missing, please tell me and i'll try to fix it.

Is it set up for coop or just solo, Vain

Scripted Solo play setup, not setup for any of the expansions yet.

Automation continues... The heroes from The Escalation is now also automated...

Copy/paste is fantastic. All the extra heroes besides the ones in The Escalation is now automated.