Very nice guide. I liked reading it. I agreed with a lot of your sentiments about the ground changes in general and also about experimenting to find what works for you best. Prior to S4, I had all my boffs using sniper rifles. That still works okay, but via experimenting, I've found that using multiple weapon types suits me much better. Specifically, I gave two boffs assault rifles, one a shotgun, one a high density beam rifle, and I kept my sniper rifle. It seems to me that the DPS a weapon does is king now; so I don't worry about having too many expose vs exploit weapons on my team.
I do have a suggestion about the Borg section, though. I have always targeted the tactical drones first. I do this for two reasons: Borg move very slowly and they do pitiful damage in melee. For those two reasons, I never worry about regular drones by themselves - they can't assimilate you without help because they can't reach you and even if they could, they don't do enough damage to drop your health below the assimilation threshold (assuming you use hypos or a medic boff to heal yourself).
When they have tactical drones as back up, however, that changes. The tac drones do decent damage at range, which means they can soften you up for the regular drones to assimilate you. That's why I pick the tactical drones first. They're the ones that can fight back and they're the ones that can actually hurt you. Negate that threat and the regular drones can be mopped up at leisure (or you can taunt them by taking five steps back every time they take one - try it, it's good fun).