1. When I place fighters on the clock from the inflight box and their "turn" comes up later, what happens if the new raid contains no fighters, or the number of fighters required is less than what's on the clock? Do they proceed back to the inflight box in this case? I'm assuming that I will always select fighters from the clock before fighters at the base, right?
You NEVER select fighters from the clock! All fighters from the clock (from space for the current time and earlier times) are moved to their airbases during the first step of Airfield Operations Phase (after Clock Update step of previous raid). So, when the new raid deployment occurs, the fighters Gruppen from the clock are already available.
2. I can have a squadron become an Ace during either step 8 or 13 of the raid phase, correct? If I promote a squadron to Ace after step 8, do they immediately get to Ace and use that advantage in step 13? Or do they wait to use the advantage in the next raid?
Squadron can become an ace squadron during hunter attack only, not as a result of squadron attack (19.41, 19.42).