1 ) I personally don't think David "created" the spores and neomorphs, in any direct sense anyway. From what we've observed regarding how the accelerant works, the higher the dosage the more violent and chaotic the mutations it causes. When the payload is dumped on the plaza we see the engineers literally exploding into mutated forms, but none of them seem to live more than a few seconds. The decapitated head in Prometheus reacts in a similar way once reanimated, belonging to one of the engineers exposed during the initial breach. Compare that to what happens to the engineer in the prologue, as well as Holloway and Fifield, who are all exposed to much smaller amounts.
As such, I think that the effects of the accelerant would have slowed as it dispersed into the wider environment over time, with mutations eventually stabilising to the point that they were beginning to form more sustainable organisms and lifecycles like the spores/neomorphs. From what we see of David's lab, it doesn't look like he had access to much technology beyond what we might equate with a physician of the enlightenment era, so I also don't think it's likely he "created" the protomorph directly either. More likely, we was conducting experiments through controlled exposure to the accelerant, along with some selective breeding, similar to traditional horticulture. Yes, it's still a form of genetic engineering, but it's very rudimentary compared to what the engineers on LV-223 must have been doing.
In a sense, he was applying his systematic rationale to the chaos that is the accelerant, but it still has an overall trajectory that ends with xenomorph-like organisms. That would explain the mural we see in Prometheus, not to mention the aeons-old wreck in Alien.
2 ) I don't think we'll ever know, but it must have been far enough to wipe out all of the engineers, or at least isolate them away from any means of contacting their kin on other worlds. Otherwise you think they would have sounded the alarm in the intervening period.
3 ) It's likely that any who survived the initial bombardment would have been driven into hiding, and probably weakened over time. Do we have proof that they were actually alive before he dissected them though? It's possible he just found and examined corpses that pre-dated his bombing raid.
4 ) I thought the Prometheus had been missing for ten years. That would imply that they arrived almost immediately, which seems to run counter to what David says in The Crossing. It's certainly possible though.
5 ) I think one of the reasons he wanted fresh human subjects was that the protomorph strain he'd bred hadn't been given a trial run yet. You wouldn't want to pack them into another juggernaut and unleash them on humanity only to find that they're a dud. Basically, I don't think he was confident taking them out of the lab yet. It's worth giving some thought to Walter's suggestion that he was actually malfunctioning too - basically going out of his mind.