There's several issues at play making this quest break at the moment; I SUSPECT something is happening where Jake is losing the "temporary follower" 'flag' before he should, which would explain a lot of issues. He's already set as Essential at all times, but you can't Stimpack-Revive 'non-followers'.
This makes sense. It could happen if certain mods like AFT or similar are in use. Or SKK Combat Settlers, I tried that mod briefly and it completely broke Jake(although on seemingly any quest, even Laying Foundations). If these mods work by applying packages/aliases to the NPCs, and maybe finding NPCs by keywords/AVs or other dynamic ways, it could interfere with stuff like temporary follower since I believe that may be working via AI Packages as well. It's possible that other mods might be forcing their packages onto Jake, resulting in SS2 packages not taking effect properly.
I've installed Cheat Terminal, and I've given myself the Spray n' Pray and enabled god mode and one-shot kill. The Gunners tend to target me, so I run south into the fray and then wipe them all out. No matter what I do, Jake still takes a hit, and I can almost guarantee you it isn't friendly fire. Since it seems so damn impossible to save him, this sounds like something that should have been caught in testing. Not trying to be too harsh but it is what it is.
MK41 Gyrojet is my favorite, I also give one to Jake. For NPC allies, Targeting Computer is very OP since their typically poor aim doesn't matter. It actually deals damage pretty quickly on automatic mode since every bullet hits plus Maximum Payload increases the damage with successive hits. When not wanting to use Targeting Computer I can have it instead with Explosive style or "Mini-Mini Nuke", for splash damage & ignoring armor/DR. With Cheat Terminal or other mods like
Useful Techincal Documents you can give it a 2nd Legendary effect since the previous are just a separate workbench mod slot.
A prototype heavy machine gun from before the war. Uniquely fires .51 gyrojet rounds, doing more damage the further a target is away.
www.nexusmods.com
You can get a bunch of allies in the area too, and this really fits quite well with the quest thematically too if you install the quest mod
Blazkowics. It adds a settlement called Blazkowics Family Settlement nearby the actual area, some of whom like Billy are Essentials. The rest were Settlers but a bit higher level than usual and they seemed to have some armor and laser weapons. Everybody will join in combat when the Gunners show up, and has a side benefit of helping avoid any Gunners potentially wandering off. I had thought for a moment that the settlement was from SS2 itself, it fit that well IMO.
ID software fanboy mod featuring doom armor, Wolfenstein weapons and armor and a short quest.
www.nexusmods.com
Here's a pic(I also used a foliage mod called "A Forest"), if I recall correctly, just behind the trees at the back is where you, Jake & Aiden talk:
If it still happens where Jake gets downed, I would try SetAV Health 10000000 since at that point if it still happens then I'd think some other scripted effects from other mods may be interfering here. I've gotten through the questline with almost 500 active plugins, although I'm careful of dynamic combat stuff and in some cases had to drop mods like SKK Combat Settlers. For dynamic combat mods, I've had the best luck by far with
Pack Attack NPC Edition. It used to have a lot of problems but they've redone it recently and it's far better now.