I'm working on a side project set in the time period from just after the Third Servile War to the assassination of Julius Caesar and I'm curious as to each man's motivations pertaining to Rome. Could one assume that their thought processes were more or less in parellel even if they were at odds with each other? What would be a good source(s) to answer this as well?
Judging motivation is a tricky thing, even when the people in question left documents behind. Caesar wrote in his Civil Wars that he found himself forced to defend his dignitas and the tribunes, and by extension the Roman people. Apparently that was convincing for his troops, but was that merely propaganda? A fig leaf to cover a true ambition for domination?
Anyway, Caesar, Pompey, and Crassus were working together until sometime around 53 BCE. Julia, Caesar's daughter and Pompey's wife, died in 54, and Crassus in 53. Pompey's actions supervising the trial of Milo in 52 might be seen as continued support for Caesar, and Morstein-Marx has an article either published or forthcoming arguing that Pompey was open to a settlement with Caesar well into 49, even after Caesar crossed the Rubicon.
Your primary sources will be Plutarch's Lives, Appian's Civil Wars, Cassius Dio, Cicero's letters, as well as Caesar's own works. Modern biographies of these guys are easy enough to find; Goldsworthy's Caesar gets mentioned a lot around here - I like Meier's better but that's a matter of taste. Seager has a relatively recent biography of Pompey. There are plenty of treatments of the end of the Republic, I would start with the Cambridge Ancient History and continue on from there.