I installed a mod having changed sins game-info files having pirates with their research files deleted. I started the mod with an already existing sins diplomacy 1.00. The pirates still have their upgraded armor and hp, kicking ass of my fully upgraded star base and planet.
The raids I go up against would kill you in seconds if you played the mod/s I play. With that being said:
1. You shouldn't be playing on such an outdated version. Always update.
2. Sounds almost like you changed the core files of the game instead of the files associated with the mod. If so, you made a horrible mistake.
3. I highlight the "use better tactics" option.
A generally good tactic is to build a starbase at the chokepoint in your gravity well. Make sure it's close enough to the building range of tactical structures so you can support or surround the structure with turrets supplemented with repair bays (2/3 is enough). You also need to ensure that structure has the backup government upgrade on it. It turns the starbase into a target for your foes to be forced to attack if they want that planet. Clustering your defenses to protect the starbase helps nicely. Remember, you can always anchor the Vasari starbase as well so it won't be an issue.