Fantastic post and a belated Welcome! Seems really well thought out. Unlike what I'll post below as some notes on my impressions thinking out loud, off all you sleuthers great post.
For me, the things that stands out the most, now that we know much more about Mollie, considering we have a better idea since yesterday the loop she may have taken on her jog, is how well planned this may have been.
The perp may know Brooklyn very well and how not be noticed, especially at night.
The perp may have struck with either intrusive or natural awareness of her habits, thus able to create or take advantage of a window in time when Mollie would not be missed.
If that is true, then why go through all this trouble to end her life?
I think the trigger for this may have been the feeling of losing her or access to Mollie, or not having a chance with her after the wedding trip.
The perps sense of owning Mollie by whatever lurking habits they had may have been extremely challenged by the idea of her flying away and returning committed, so a plan may have formed over time, was maybe even tested. Like she ran into this person before on her jogs, maybe chatted in a friendly way.
A well planned perp would perhaps not leave her initial reaction to chance.
Did Mollie ever say she ran into an unexpected acquaintance during her jogs?
If this is true, then the perp may have resources, may be very technically adept at covering their internet tracks, as Otto mentioned, an IT pro on some level, who can make it seem she did homework that night, sent a snap chat, planned distractions, able to cover their tracks online.
If this is true, then the time window that was taken advantage of was in part to confuse the search and get away.
If any of this is true, could it being summer and the perp not being noticed in any way mean they too are on summer vacation, thought to be away?
Sorry for the mess above, just wanted to get it down, it is probably all wrong.