The numbers are a lot tighter in SF than in PF. A +1 or +2 in this game ends up being a pretty big deal for players in the moment.
With a Party of 2-3, you're probably going to have to make some adjustments. The first fight is probably fine, as is, because the gang members should mostly be shooting at each other, not the PC's. The fight in the fusion queen should probably have fewer mooks though and you may need to split up Ferani and Hatchbuster as the two of them together is a challenge for a party of four. You'll definitely want to take a look at the Akatas because they're dangerous even to a party of 6, especially once someone catches space herpes. I'd probably reduce their hitpoints a little and ER to 2, and maybe reduce the DC of the disease by 2 to compensate. Even with a party of 6, I had to pull punches a few times during the fight and fudge some stuff for the party.
Mostly though, you're going to want to let them get away with taking more 10 minute and long rests, and encourage them to be methodical rather than rushed.
The first book in this AP was written before the rules were completely finished, so it's a bit harsher than I think was intended. And it was intended to be harsh. Rob said at Gencon that when he was writing it, he wanted it to be deadly (but he thinks he may have gone farther than intended because of the rules being in flux). It's a harsh universe, and as a long time 3.5 player that's used to every fight being a cakewalk for my super optimized characters, I for one, can't be happier about it.