i noticed that pirate fleets dont have much pirate ships anymore and i can buy other mods ships at the jangala military shop
That's the whole point of the mod -- more variety. There's no reason that other factions might have a couple of the other factions' ships laying around. Almost nobody in this sector is doing well enough that they can afford to throw away perfectly good ships.
That said, if you don't like that, you can disable fleetIntegration and/or marketIntegration.
when entire pirate fleets are nothing but high tech and mod ships its kinda hard to get started
I am thinking it just needs to have the rates tinkered with
You do realize that mod ships can be
worse than vanilla ships, right? Junk Pirates and PACK ships, which you've likely seen as "mod ships" in pirate fleets, are generally pretty weak. For the sake of curiosity I generated some maximum-quality-factor pirate armadas, and the result involved a mix of Tiandong; Junk Pirates; PACK; various low tech, midline, and high tech ships; and a smattering of other factions like Imperium, Scy, and Blackrock.
They're kitchen sink fleets and they don't have very good weapons, either. Even this example is an extreme case in case a pirate market somehow has 10 stability.