I'm writing this guide for the Abyss of the Shrine Maiden as I think many, if not most players will have trouble as the game stops giving you clear directions for your objectives in these later areas.
I'm not writing about every map, as I think most of you got used to progressing through them from the maingame. Instead I will be writing down instructions and specific directions for every point the game blocks your path forward.

Before starting with the walkthrough I want to address the difficulty of these additional areas.
If you are having trouble with the sudden jump in monster difficulty in the Vulcanus Citadel, I have a few tips and recommendations below that should allow for easier progress.

The most simple and effective way to boost your characters damage at the beginning of the post game story is to unlock the skill fusion system. As you start the chapter 1 of AotSM you will have access to first tier, lvl3 skill fusion which will provide you passive +500 atk buff along with few other bonuses.
For unlocking the skill fusion you will first want to make 2 man party with character of your choice, then find your party member in town and interact with them to "take them for a walk". When you have your partner in tow, go find Argo in the town to talk with her and you should get a quick rundown on the SF system. Now you can interact with Argo and pick skill fusion, start quest, attacker. Afterwards interact with your partner and pick skill fusion to see the requirements and progress of the quest.
With the attacker skill fusion you should have enough atk stats to comfortably kill the story enemies, once you reach chapter 2 you should visit Argo again and repeat the process to unlock the next step level 4 buff.

Depending on how fast you blazed through the maingame this may be a huge problem.
FIrst of all there's couple buff skills you absolutely should have at this point, Brave Soul (maxHP +50%!) and Defensive Stance (Huge HP regen).
Then if you have around 50k unbuffed HP you will be able to withstand several hits from the minibosses and allow for pretty smooth progress.
As the really good HP boosting equipments are available only after you advance to the later areas in Vulcanus citadel, I recommend you wear the "green" quality armors you got from Stalwatos Ruins events, if you want you can repeat some of the duels to get better stats on the pieces.
In the Seldona Laboratory the northern blue chest can drop accessory piece with about 50Vit and once you gain access to the southern part the chest in there has both boots and necklace with little HP bonuses. Once you reach Asham Extractor you can get some really powerfull HP boosting chest piece and boots from the chests there, if you made it here you won't have to fear death anymore.
Before you have access to the better gear from Vulcanus Citadel you may have to resort to the other way of increasing your Max HP, that is leveling up. If you are still below lvl50 I highly recommend you level up to 60 atleast, you will see big HP gains after a breakpoint at 50. Safe way to level up is to chain kill monster in the previous Stalwatos Ruins area and later move to Vulcanus citadel so you can get some loot from blue chests at the same time.

Now for the actual walkthrough:

Run through the first area as you see fit.
Once you reach locked gate in Seldona Laboratory, backtrack to the large graveyard in western part of the same map. Look on northern side of the graveyard for Aldano's gravestone (bossfight).
Enter Blazerock Fortress to the south and interact with the stone tablet marked with (!) for your next objective.

Enter the Bardette City from Seldona Laboratory. In the Northern part of the map look for a well in the middle of ruined buildings, it has a white lantern to mark the spot(boss fight).

Look for a green spirit NPC in the southern most part of Seldona Laboratory, after obtaining a quest item run back north and look for marked grave on the right side of the road. It's placed in the area with 2 gates and you will encounter easy fight.

From Seldona Laboratory entrance backtrack into Magmatite Research site. Look for a ruined building nearby, where the green treasure chest is on the map(boss fight). Afterwards teleport to this area's entrance and look on the left hand side while following the road for a quest marker (?).

Enter the Blazerock Outer Wall from Bardette City. First time in the area you will have to do some running around for events and to open they way forward.
First follow the path south until you encounter locked gate.
Then run to the north eastern room with 3 sword NMs, there should be short event so check the northern wall just left from the entrance for hidden room and another event. Also pull the nearby lever while you are at it, just ignore the lvl 150+ NM guarding the red chest.
Follow the path around to the south east room with a yellow marker in it. Talk to the NPC and grab the warehouse key from behind it.
Run to the northern part of the map and follow the path that leads south from the entrance to a seemingly empty area, look in the left side room for the 4th and last key.
Now while you are still in the area you can choose to unlock the path to the next map in this area. Make your way back to the middle section of the map and enter the locked room to east with you warehouse key. There you will find lever guarded by a NM monster which will unlock the gate from the southern exit. Also in the other corner of the room you will find a key item [Mining Explosives], this will be Required to progress later on.

After you obtained the keys and unlocked the teleporter in Kikoth Excavation it's time to head back to Blazerock Fortress and unlock the way forward.
In Blazerock Fortress pull the two levers near entrance and run to the north east exit. Progress through the next area into Asham Extractor to receive your next objective from a nearby tablet and bookselves.
Run to the northern part of the Asham Extractor map, look in one of the buildings.
Warp to Kikoth Excavation unlocked after BLazerock outer wall. Follow the west side of the map and loo for a cave you can open with the [Mining Explosives].
Go back to Blazerock Fortress, make your way to the northern lever and operate it. Now take the southern exit to the Clastdale Caves and check the door in the southern part. Go back to Blazerock fortress again, check the room west from the middle of the map for a key item [Lake Key], no need to kill the bosses in the area. Go back to the Lake for the last extractor.

In Acropovale Ruins numbering the levers from top down and left to right.
To unlock the way forward ignore levers 1-3 and run to the lever no. 4. Pull the lever No. 4 and backtrack to the lever No. 1 and pull it also. Now you can take the eastern path to a room with a few lover level NMs.
After you got the key run back to lever no. 1 and pull it again to open the way south. Ignore the other levers and use they key to open the way forward, when you encounter second locked door look for unexplored room nearby and beat another NM for the second key.

In Gardens of Calamity there's couple gimmicks with magma slimes that turn into crystals when killed. If your path is blocked by big crystal wall you need to kill slimes to produce small crystals until you get a message that the area heat has increased. To remove the boss' shield you will have to first kill the slimes to produce crystals, then activate them.

Rest of the Volcano area should be pretty straightforward, if you need any other directions leave a comment and I'll update the guide.

Start by making your way to Greyfort: Middle Level.
Here you will need the new scanner skill obtainable from the GOddess statue in Stalvatos Ruins after beating the 1st chapter. As you move in this map look for semi transparent enemies in side paths and other seemingly dead ends.
The Upper Level has moer of the invisible enemies blocking your way. Once you have seen the events at Fiernia Sanctum you can start looking for this areas "keycards".

After seeing the even at Fiernia Sanctum teleport back to Greyfort: Middle Level and explore the empty room in south east corner.

Head to Valenstar Center. Explore another empty room south east from the initial large area for the charm. To unlock the way forward you will have to visit each 4 of the exits in the first part of the map and look for a invisible creature carrying a key in each one.

With the Snow and Humanity charm at hand, you are ready to head to Fiernia Sanctum again. Use Humanity to open the first door, once you find a teleporter use Snow charm to access it. Work your way south to Sacrifia Sky Chapel and use the teleporter at the south wester end of the map.
Inside a ruined building in Stragorn Sand Wastes you will obtain the last charm, Sword.

Even with all three charms you still won't be able to activate the next teleporter in the Sacrifia Sky Chapel. Instead you will have to make a detour to Oltado Cloister and activate the altar there using the charms Sword, Snow, Humanity (Bottom to top).
After you enable a bunch of floating platforms and need to use them to reach the building at the western end of the map where the green treasure chest is also located. Once you reach the building you should use the altar to turn your Humanity charm into a Beast charm.
Finaly with the charm combination Best, Snow, Sword you will be able to activate the teleporter in middle-north of Sacrifia Sky Chapel. Now you only have couple straighforward maps left and one of them requires you to kill 4 monsters in a correct orders, but the numbers are marked on the walls behind them.