I think the prism freeport is still looking for the weapons you removed. If I try to go to acheron's domain I get an error that the nailer can't be found and then a CTD after jumping in. Here's the log:
136097 [Thread-4] ERROR com.fs.starfarer.combat.CombatMain - java.lang.RuntimeException: Weapon spec [SCY_nailer] not found!
java.lang.RuntimeException: Weapon spec [SCY_nailer] not found!
at com.fs.starfarer.loading.Q.Ô00000(Unknown Source)
at com.fs.starfarer.loading.SpecStore.o00000(Unknown Source)
at com.fs.starfarer.loading.SpecStore.o00000(Unknown Source)
at com.fs.starfarer.settings.StarfarerSettings$1.getWeaponSpec(Unknown Source)
at com.fs.starfarer.api.impl.campaign.fleets.DefaultFleetInflater.inflate(DefaultFleetInflater.java:232)
at com.fs.starfarer.campaign.fleet.CampaignFleet.inflateIfNeeded(Unknown Source)
at com.fs.starfarer.ui.impl.StandardTooltipV2.createFleetTooltip(Unknown Source)
at com.fs.starfarer.campaign.C.super(Unknown Source)
at com.fs.starfarer.campaign.CampaignEngine.advance(Unknown Source)
at com.fs.starfarer.campaign.CampaignState.advance(Unknown Source)
at com.fs.starfarer.BaseGameState.traverse(Unknown Source)
at com.fs.state.AppDriver.begin(Unknown Source)
at com.fs.starfarer.combat.CombatMain.main(Unknown Source)
at com.fs.starfarer.StarfarerLauncher$1.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
As for adding factions to Prism's stock via prism_factions_whitelist.csv, I've managed to add sylphon but can't get others working. For example adding 'dassault', 'dassault-mikoyan', 'dassaultmikoyan', 'DM', and 'DME' all fail to add Dassault-Mikoyan Engineering ships. Do I need to dig through the respective mod folder to find what I need?