The issues below don't appear to cause any in game issues but I wanted to point them out if not already known.
Missing sounddata entries
PlayerTec.entity, PlayerPsi.entity, PlayerPhase.entity
GameEventSound:CannonUnderConstruction "UI_COMMON_CANNONBUILT"
AbilityGravityWarhead.entity
sound "GENERIC_WEAPONFIRE" (is missing from Vanilla also)
AbilityChargedMissiles.entity, AbilityChargedMissilesLight.entity,AbilityPhaseCloak.entity
soundID "EFFECT_PhaseCloak" (is missing from Vanilla also)
Miss-spelled effects due to capitalization (doesn't appear to matter in windows, was just an obvious type mis-match)
AbilityMeteorStrikeShips.entity (actual file named Ability_MeteorStorm_Self.particle)
smallEffectName "Ability_MeteorStorm_self"
largeEffectName "Ability_MeteorStorm_self"
BuffFarSight.entity (actual file named CapitalBuff_FarSight)
smallEffectName "CapitalBuff_Farsight"
largeEffectName "CapitalBuff_Farsight"
BuffPhaseGateStarBaseSelf.entity (actual file named Ability_PhaseGateStarbase-Buff)
smallEffectName "Ability_PhaseGateStarBase-Buff".
largeEffectName "Ability_PhaseGateStarBase-Buff".