Stuck as hell - with NPCs not spawning!

Mole's absence after Agroprom is a known issue that has been with us for some time.  He is supposed to reappear at Bes' camp fire in the north west of Dark Valley, but he seldom if ever finds his way there now. If you weren't able to hand in his "Find Mole's lost PDA" task while he was still in Agroprom, you can force it to complete using info portion agr_krot_PDA_done. However, you won't get his reward of a PPSH-41 sub-machine gun plus ammo. This isn't a big loss as you will undoubtedly have better weapons by now, but you can always spawn it in if you want to see what you missed.

Krysjuk "The Rat" appears when you enter Cordon through the tunnel from Dark Valley after receiving the task from Borov. He emerges from the Old Workshops (where the Bandits are usually found) and heads over to the barn by the old cement factory. He remains in the side area there until you get him the permission that he wants. If he dies, you may be able to complete Borov's task by spawning in Krysjuk's PDA (pda_krysyka). If Borov won't accept this, the whole point is to get his reward, a stash containing a Bandit Exo suit - one of the items required for Akim's main task, which leads to finding the parts for the SKAT15 outfit. If you don't have Borov's stash, you can spawn the Bandit Exo from the ESC-S Outfits tab - I think it is exo_bandit_outfit - and hopefully Akim will accept this. If all else fails, there is a section for spawning the SKAT15 parts in the ESC-S Items tab.

Kostya's quests are a string of find-the-item tasks that are fun but don't affect anything else. I don't know how far you got with him, but after your first meeting in Cordon he moves on to several other locations - the camp fire in the vehicle scrap yard in The Dump, the camp fire in the Bar close to Arnie's room, and finally the camp fire in Army Warehouses where Wolf is also found. Kostya doesn't move again from here. If he isn't at any of these locations, you could spawn his tasks via the info portion list, but I really don't think it would be worth the effort.

Guide is the only key NPC in your list, because you need him to find Doc and the decoder to the locked door in the Sarcophagus. After you find Ghost's body in X-16 you get a task to "Talk to the Guide about the Doctor". Guide should then appear in the destroyed farmhouse in The Cordon where you met Fox. If he is no longer there, info portion esc_find_doctor_start should bypass him and start the "Meet with the Doctor" task. Doc should then be waiting for you in Strelok's hideout in the Agroprom Underground. However, I don't think you will get Guide's convenient transition from Cordon to Agroprom, as this is spawned by a function within the game's code. Fortunately other routes are available...