Bonuses from Items
I think one list of bonuses will be simplest. They can then be applied directly to the character sheet. The different types of bonuses can be unlockable too. So that in version 1 there are no possible bonuses. Later in the game then when your items have enough sentimentality to receive a bonus only the bonuses that have been discovered can be applied.
Damage soak, of each type
Damage resistance of each type
Learning aid; increasing the learning rate of one scalar/proficiency.
Damage bonus fixed or %
Scalar nudge, shift a skill in one direction whilst equipped/held
Reputation bonus for equipment of that race/class/civilization (do I really want this though)
No strike that I have only seen it a few times and it did not add much. On the other hand Set items could be nifty. ie Dressed like a Trinitarian.
Normal disruption, Change the way the skill checks work.