Unofficial Fallout 4 Patch

I can confirm that the regulator is missing and disabled in your save, but have no idea why that would be the case. The patch also can't be the culprit because it doesn't edit the quest or the spawn marker.

You say that UFO4P can't be the culprit but did you try disabling the patch before entering the room with the regulator? That's literally the only way I was able to get it to spawn in without turning off survival difficulty.

No, that's not a valid testing method. You can't remove the patch or any mod on an existing save without it causing irreversible save damage. If that's something you've been doing then that's more than likely where your problem lies. You'd be surprised how many reports we get of people claiming that removing the patch from their load order fixes a bug when in reality it turns out to be something else that is to blame.

Funnily enough I hadn't disabled a single mod mid game until I encountered this bug. I have less than 20 mods total, most of which are cosmetic and none of them touch Far Harbor other than this patch. I did end up disabling/re-enabling this mod for 1 loading screen so I could continue my play-through without wasting any more time waiting on a fix that will never come, I've had no problems so far.

I've also encountered this bug. I've never disabled UFO4P, so this can occur under pristine UFO4P conditions. Since UFO4P doesn't modify that quest, I'd say this is a vanilla bug. I was able to backtrack the issue to when I was doing Call to Arms, but that's probably just coincidental. At that point, I hadn't done anything with Far Harbor.

This bug is a little pernicious, because the pump regulator is created by DLC03CoA_FFNucleusQuestObjHandler at the beginning of the game. The bug can occur silently, early in the game, and then only be noticed hundreds of hours later.

Perhaps one solution would be to modify the Papyrus fragment for stage 10 of DLC03CoA_FFNucleus03 to check whether the pump regulator is deleted (it's not just disabled). If it is, then a new pump regulator can be created and the alias replaced. There are also pump regulator aliases in DLC03CoA_FFNucleus03_PumpHandler and DLC03CoA_FFNucleusQuestObjHandler. I don't think these aliases need to be updated to fix this bug, though.

This might be a few years too late for OP, but as a temporary workaround, you can drop out of survival, use the console to create a new pump regulator and advance the quest to the next stage, use the console to re-enable enabling survival, and then re-enable survival:

Player.AddItem 0302b5d9
SetStage DLC03CoA_FFNucleus03 20
cgf "Game.IncrementStat" "Survival Denied" -1

Another console workaround that's more like the suggested fix. This must be done after starting the quest:

03057148.PlaceAtMe 0302b5d9
plr
ssq DLC03CoA_FFNucleus03
ForceRefIntoAlias Pump