Basically, I liked the setup for F/P part 1 but I thought the monster was out of character for the scenario and there was no way I could credibly deliver it to my players and keep the horror/suspense going, even if I obfuscated its origin. 

I finished a Masks of Nyarlathotep campaign back in February. In the campaign, the PCs' patron was a Dr. Larson, who was a human possessed by the mind of a serpent person. So, at the end of Masks, I had Larson open a gate at Gray Dragon Island, allowing a few PCs to escape before the rocket chamber blew up.

Here's how I reasoned it. The Larson serpent person had a great deal of timetravel / foreseeing ability. Its physical body was woken up in Chester Ohio as stated in the future perfect scenario, assuming Arthur Hunt's identity. However, it knew that it would probably die in 1952 and could not foresee a way to get around this unless it gave up its plan to open a permanent time gate, which it would not do. So, it hedged its bet by having a mental virus implanted in a mythos tome. This virus was a modified shrivelling spell. Each time the sorcerer used the spell, part of its mind was replaced by a duplicate of the Larson serpent person. Eventually, a Dr. Larson was taken over in this manner during the course of the Masks of N campaign. Dr. Larson's plan was to create a way for the physical serpent person to be resurrected after the 1952 explosion.

Dr. Larson saw the investigators in the Masks campaign as a perfect tool to achieve this goal. He saved them after the conclusion of the campaign and killed them off or corrupted them into working for him. They formed an organization that would resurrect Arthur Hunt. During this time, Arthur Hunt is ignorant of the specific actions of the Larson copy, although it is aware of its existence.

However, Nyarlathotep was not pleased with the creature interfering with its plan and resurrected an investigator from the Masks campaign and sent him against Hunt. The investigator was a French gun runner and eventually managed to cause the imperfection in the golden cube that caused the explosion in 1952.

However, the serpent person knew that the gun runner was going after him. It foresaw that the gun runner could not die until it had killed Hunt. At first, it was a normal man, but Nyarlathotep's power would mean it would become monstrous and more powerful after each death. It would absorb the life force of nearby creatures into it, becoming a gestalt creature. Eventually, it would become a god in its own right.

Hunt let the gestalt creature kill it the first time in 1952, believing that would kill the thing. However, it didn't quite work. Gestalt phased out of time but phased back in time in 2005, as a mindless beast. Gestalt killed the first two victims and regained some semblance of humanity and intellect. At the start of the scenario, it has figured out how to separate parts of itself and has absorbed some animals from different time periods in the area. It is now attuned to the time gate and can't move more than 150 miles away from it.

I will run parts 2-4 straight from the notes and plan to end it with a scenario aimed at the Larson organization.

does that make sense?