So, here's an idea. Maybe we can do some minor timescale retconning? Simple version; It took Daniel and Simon roughly the same time to get back from their failed expedition down in the Lost Hallways (Maybe the correct combination is North, West, South, West?) as it took the rest of the crew to have their misadventures. In other words, Daniel and Simon get back just in time to see Jonathan and Lily/Popoi meeting again. From thereon, we can do some party regroupin/splitting.

Lily/Popoi wants to stay with Devon (The Templar lady), pretty much the only person she trusts right now. Maybe you can take over control over her? 
Jonathan wants to stay with Lily/Popoi
Marik wants to join again.

All other players can just go somewhere else.