My friend, I am afraid that if you are trying to accurately quantify the number of imperial civil wars that occur then you're in for a hard time. In the fluff there are many different examples of civil wars in the Imperium; it is essentially a colonial empire of a million worlds where communication and trade is regularly lost etc. However we must take into account that many civil wars would be subject to suppression by the Inquisition and thus not recorded. If you feel you want to play a loyalist vs loyalist campaign then feel free to write your own.
Then another issue is "what constitutes a civil war". A civil war is defined as "A war between citizens of the same country". An issue I wish to clarify is whether Space Marines are really considered part of the imperium. They are autonomous, independent and outside the normal chain.... A civil war can also be between two successor states of a nation to the Badab Schism is fine (the astral claws and their domain seceded from the imperium before the war propper)
Other examples I can think of are
The Battle for Kronus (Blood Ravens Chapter vs Imperial Guard; WH40k DoW)
The Months of shame; just after the first war for armageddon (Space Wolves vs Inquisition, Grey Knights and Red Hunters space marine chapter). I'm not sure if this counts as there was no "war" but battles were fought and warriors died.
Pretty much every battle that the Soul Drinkers took part in (Sould Drinkers Novels)
Fenright Tithe Wars (also involved aliens)
Fourth Quadrant Rebellion
Might I echo CotE and ask the purpose of this?
A fan of the clasics; MK VI power armour for life
Keep in mind you are arguing "realism" about an army of genetically-altered supermen that are able to shrug off rocket propelled explosive bullets because someone is waving around a cup full of blood that reminds them of their long lost Super Daddy that was killed by there Extra Special-Super Uncle.