Hmm, I currently at sector 52(53 kill me in new special way...), and I can't remember any special except difficulty wall before some previous update was appeared.
Just make challenges to boost other aspects and go be stronger.
Personally I choice synth as primary target to upgrade.
don't forget crew, energy technician can really ramp up your reactor boosts. I like synth as a priority to upgrade as it's easy to see progress in some fashion.
I was nearly maxed out before crew update, I think the issue with 48 is the long range ship, which I'd advice some charge lasers or bomb launchers for their range buffs if you're struggling with them. But since that message is from 6 days ago I think it's no longer an issue.
I think 48 was difficulty walled before update, but I beat it just as update released, and after stopped at ~52 (in one strike) I was inspect for new features and now I still at 52 working with crew etc...
Well I hope you get through your current wall soon and punch through to the next base to get resources growing on that. My setup for a long time has been 4 beams with 2 laser cannons in support mode, but I may have to rethink that setup.
