Does the option to move units with mobility occur before or during the action window in between 3.1 and 3.2?

RRG Mobility section covers it. Treat it like a reaction to the combat phase starting (but before other reactions). Reactions to a framework event (such as 3.1) resolve before moving on to the next framework event (being the action window opening), meaning any/all Mobile must happen before that action window opens.

The short answer to your question is that Mobility occurs before the action window between 3.1 and 3.2. In fact, the detailed explanation for 3.1 in the rules text (p. 25), indicates that Mobility takes place as part of 3.1.

The shorthand that PBrennan offers ("Treat it like a reaction to the combat phase starting (but before other reactions).") is generally true, but not the way I would go. It implies that Mobility should be treated as a "triggered ability," so may not be completely accurate in all situations. The difference could wind up being important. For example, something that could cancel Reactions could not cancel Mobility.

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For reference:

"Mobility" from RRG, p. 10: "After the combat phase begins, each unit with the Mobile keyword may move to an adjacent faceup planet. This occurs before any reactions to the beginning of the phase."

"3.1 Combat Phase Begins" from RRG, p. 25: "This step formalizes the beginning of the combat phase. Units with the Mobile keyword may move to an adjacent planet at this time, before reactions to the beginning of the combat phase can be initiated."

Just to piggy pack on the topic of Mobility... Do units that utilize it and other movement actions (like the Eldar Wildriders), will retain their state after movement? The only time movement changes card state (exhaust) is committing to a planet with the Warlord?

Cards retain their state when they move unless the effect that moves them specifically says to change their state (like committing units from the HQ to a planet along with the warlord during the Command Phase).

Cards retain their state when they move unless the effect that moves them specifically says to change their state (like committing units from the HQ to a planet along with the warlord during the Command Phase).

Just realized I totally missed this rule in the first few plays!

If both players have units with mobility I assume the player with initiative decides weather and where to move all of their units first? Then the other player decides what to do? The player with initiative can't pass and then use mobile if their opponent does, correct?

Correct.

RRG, p. 10: "If there are multiple Mobile units in play, the player with the initiative resolves each of his Mobile units first, followed by his opponent."

Thanks.

I really need to read the actual rules one day.....

Meh. It's a glossary. Why read when it's indexed?