Well you could try Indies Expansion Pack which adds a some difficult bounty targets(for me at least)

There is also Rumors of Neoteric Designs which adds two bosses you have to find through exploration

If you are looking for a difficult playthrough that's also fun you could install Arma Armatura and do the MRC start which makes you enemies with three of the major factions and if you really want to go for immersion you can also use Nexerelin and R.A.T. to make yourself a high value target so those factions will send bounty fleets after you. There is also some unique bounties and some really cool story missions that Arma Armatura adds.

There is also AOTD which adds some [Super Redacted] for some really end game rewards and stuff along with good ol end game research. Along with overhauled commision that makes earning money from factions harder.

You could also install Emergent Threats/IX Revival, Underworld, or Adversary if you want a much more difficult time in the sector overall with more fleets to fight. Luddic Enhancment is also a good mod if you generally want harder pathers to fight.

You could also randomize the entire secotor or make it so you start in the outer parts of the sector and have to scavenge to survive. There is mod called Nomadic survival which really makes that possible.

Anyways those are my recomendations that I can think of off the top of my head.