@inspirationxvii First things first. If you get infected by a worm you turn into a multi-eyed monster that tries to infect other lifeforms (or open a portal). So, with that clear:
1) There are two alien races. The original one is already extinct because the second one (the worms) had turned them all into monsters. I'm going to call the original race that lived on the other world aliens and the infected forms monsters. The old monster is probably, like monster Flare, an infected alien who still managed to retain its personality. It summoned the girls to kill it (like Flare herself later did with Aimi), which is misunderstood by senpai. It used the last of its strength to send Flare (or a piece of Flare) to meet Aimi in the past.
2) Well, judging from what happened to her friends Tamura and Yuyama in chapter 14 her soul would eventually just move on after accomplishing her goal.
3) She just turned into a monster like everyone else who got infected, but like the old alien she managed to keep her personality enough to ask Aimi to kill her.
4) The gas kept piling up because they never managed to get to the point where they could blow up the tower until that penultimate loop. Blowing up the tower was the key to changing the conditions of the loop just enough to start trying to break the loop. Probably in previous loops the divergence point was when Aimi met Flare at the opening just before the beast went nuts and ate her. That would have been the point in previous loops when Nako died and Aimi was forced to abandon Flare. When senpai saw the tower the first time in the final loop she saw it being reconstructed. There is no indication that this happened in chapter 6 when she and Flare were trying to go to the other world the first time.