Being the first time I have dabbled in this area I do have some questions. Firstly if I start the game with just one race (player race) and then create more races using SM can I then turn them over to the computer to run as an NPR and will they then function fully as per any other NPR that had been created by the game?
No. Player-controlled NPR are different from computer controlled. The computer has to create and start with control of any NPR it's going to run.
Secondly I understand how that any NPR that is pre trans newtonian will simply lie about on their planet waiting to be squished. But is the Trans newtonian tech the only one needed to trigger an NPR into playing and growing like a full player race? If I create a new empire and SM them just the TN tech before turning them over to the AI will they function fully?
moot due to 1
Finally regarding the peace counter clock, does this apply only to races who have been created at exactly the same moment as each other (for example two NPR's who appear on two planets in the same system). Or can I create the new factions on Earth before doing any sort of time interval and have them all obey the peace accords as set by the game options to begin with?
Don't remember - you should be able to find Steve's original posts about the peace counter clock in the Mechanics threads.
John