All the times I have run it the players managed to complete the scenario in about 5-6 hours. In all cases -for different reasons- I had to almost omit the third act because the players took things in a way that made it difficult to enter the third act and, when they did, things came to a close much faster. Depending on what they do it may be that the session could be much longer or much shorter, but so far in my experience 5 hours is doable.
Any chance to get it down to that did you cut anything out?
I will admit that like you I had to think up how to do the 3rd act. As by the end I couldn't do it as written.
I followed the script as much as possible, but my players actions forced me to adapt and change things a bit: on my first game they refused to leave the Montero and only explored the Cronus in groups of two -and they were VERY lucky with the dice-. Things were moving slowly and then they managed to get some black goo into the Montero. At that point, I decided that Mother would trigger the self-destruct of the Cronus, instead of the montero, as the mission critical item was already on the Montero. It worked well, they panicked, they were separated in different groups in different places and they struggled to get back to the Montero, get everything running and get out, but then the android revealed itself and all went south. Great fun. The Sotillo wasn't even needed.
In another game the players divided themselves in different opposed groups in Act II (with the NPCs mixed with them, slowly turning violent). They played a game of rat and mouse with one another and the neomorphs. By the time when we got into the third act almost everyone was dead and when the Sotillo arrived with the new characters, all hell broke loose, everyone tried to seize the opportunity to save their lives and things moved very fast.
Another game I ran was pretty much the same, it went slow at the beginning but then everything started to go badly very fast in act II, I just let it play out because everyone was having fun; so I didn't introduce the Sotillo, as I didn't feel it was needed.
I'd like to run it again with a group that takes more time and really thinks things through (a lot of my players were very impulsive), but as long as everyone is having fun, just adapt to what you see fit.