So I've decided to look at some of the issues I've discovered in game that seem like errors. Some MAY be working as intended but they don't make sense to me so I've changed them for now. Here is a list of some of the "workarounds" I've made. I'll try to clean it up later and add some more but it's bedtime, there's a couple of credits to add also 
Fixes for:
- Cultural traits granted to one too many colonies
- 2nd Trader Ideology not granting trade bonus
- Orbital Specialization 1 and Logistical Optimization 3 are not granting bonus military production (logistical may have been intended to be shipyard decay but the code was closer to military production so I've gone with that for now). This seems to affect all tech trees.
- Hyperion Supply System and Hyperion Shipyard aren't granting level bonuses
- Mega Resort and Biomass Resequencer unbuildable, Food Distribution able to build after upgrading
- Trade buildings aren't granting level bonuses
- Tidally Locked worlds aren't granting trade bonus
- Research Cloisters, Quantum Research Foundation, Ascension Gate anomalies (granting total faction research bonus seems very unbalanced)
CultureTraitDefs>
AffinityTrait2, AffinityTrait3, ProminenceTrait2, MotivationTrait2, MotivationTrait3: Set Stats>Target>TargetOrdinalConstraint
GreedTrait2: Set Triggers>PerformAction>ValueParam ***the first one***
Reduce values by one, ie 1 to 0 or 5 to 4
CultureTraitDefs>InternalName: TradersTrait2
Problem: Not giving trade route bonus
Cause: Stats>EffectType incorrect "TradeRouteIncome"
Cause: Stats>Target>TargetType incorrect "Colony"
Solution: Set Stats>EffectType to "TradeRouteValueRaw"
Solution: Set Stats>Target>TargetType to "TradeRoute"
TerranTechDefs>InternalName: TerranOrbitalSpecialization1 (affects other tech trees too)
TerranTechDefs>InternalName: TerranLogisticalOptimization3 (affects other tech trees too)
Problem: Not providing military bonus
Cause: Stats>Target>TargetType incorrect "Ship"
Solution: Set Stats>Target>TargetType to "Colony"
Improvement>InternalName: HyperionSupplySystem
Problem: Level effect not working
Cause: LevelEffectTriggers>Lifetime set to "Instant"
Solution: Set LevelEffectTriggers>Lifetime to "Target"
Improvement>InternalName: HyperionShipyard
Problem: Level effect not working
Cause: LevelEffectTriggers>Lifetime set to "Instant"
Solution: Set LevelEffectTriggers>Lifetime to "Target"
Improvement>InternalName: MegaResort
Problem: Unable to construct
Cause: Prerequ>UpgradesFrom incorrect "Amusement Park"
Solution: Set Prerequ>UpgradesFrom to "AmusementPark"
Improvement>InternalName: FoodDistribution
Problem: Able to build again after upgrading
Cause: Preclusions>Improvement incorrect "XenoIrrigation"
Solution: Set Preclusions>Improvement to "XenoIrrigation "
Improvement>InternalName: BiomassResequencer
Problem: Unable to construct
Cause: Prerequ>UpgradesFrom incorrect "XenoIrrigation"
Solution: Set Prerequ>UpgradesFrom to "XenoIrrigation "
Improvement>InternalName: TradePost
Improvement>InternalName: TradeCenter
Improvement>InternalName: CustomsOffice
Improvement>InternalName: GalacticBazar
Improvement>InternalName: TradeCapital
Problem: Level effect not working
Cause: LevelEffectStats>EffectType incorrect "TradeRouteIncome"
Cause: LevelEffectStats>TargetType incorrect "Colony"
Solution: Set LevelEffectStats>EffectType to "TradeRouteValueRaw"
Solution: Set LevelEffectStats>TargetType to "TradeRoute"
Improvement>InternalName: ResearchCloisters
Improvement>InternalName: QuantumResearchFoundation
Improvement>InternalName: AscensionGate
Problem: Giving total faction research bonus
Cause: Stats>Target>TargetType set to "Faction"
Solution: Add Stats>Scope to "Global"
Solution: Set Target>TargetType to "Colony"
Improvement>InternalName: AscensionGate
Problem: Not an upgrade of QuantumResearchFoundation
Cause: No Prerequ
Solution: Add Prerequ>UpgradesFrom to "QuantumResearchFoundation"
PlanetTraitDef>InternalName: TidallyLockedWorld
Problem: Trade route bonus not applied
Cause: EffectModifier>EffectType>TargetType incorrect "Colony"
Solution: Set EffectModifier>EffectType>TargetType to "TradeRoute"