Re: So the lb lineup
My best guess is that in the "base 4-3" alignment, Brandon Spikes will continue to play MLB. Hightower will likely take over as an every down player (or close to it) at either SLB or WLB. He has the versatility. Where he plays in the 4-3 will likely be determined by who the 3rd Linebacker is. Dane Fletcher can play any of the positions, as can Jamie Collins, though he has primarily been the SLB.
In Sub Packages with 2 linebackers, I expect Hightower and Spikes to be the predominant pairing in run situations or when they want to blitz, and either Fletcher or Collins in passing situations due to increased athleticism.
When the team transitions to a 3-4, Rob Ninkovich usually stands up and plays one of the OLB positions. Hightower has normally manned the other, and he still could, but I wonder if he'll stick inside now with Spikes and the team will tap Jamie Collins' past ability as a pass rusher.
There are a lot of possibilities, and the coaching staff probably won't know how to proceed until the bye week.