I have by no means play tested every iteration or game mode of the proposed custom rules below.

TL:DR.

Randomly roll an encounter set and add it to the deck! Suddenly you might need to deal with Byahkee's in your Study, Rats in the County Express or Naomi's crew in the heart of Carcosa! All of the rollable encounter sets are scenario neutral or altered to function in any scenario.

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These are the rules:

Only ever gather Treachery cards and enemies that do not have acts or agendas on their flip side (or would otherwise be given away by their flip-side). Never gather cards that refer to named locations or unique location types (Such as "Altered" or "Historical Society"). Never gather cards that refer to information in the campaign log unless you are playing the relevant campaign).

Never gather cards from a Scenario that you havent played yet!

Re-roll any result involving cards you do not own.

After gathering encounter sets for your scenario roll a d100 until one of the numbers below is rolled, gather the appropriately numbered encounter set and add it to your scenario's Mythos Deck. Re-roll until an encounter set that has'nt already been gathered is rolled.

1- Dark Cult
2- Rats
3- Striking Fear
4- Ghouls
5- Anchient Evils
6- Chilling Cold
7- Nightgaunts
8- locked doors
9- Agents of Hastur
10- Agents of Yog'sothoth
11- Agents of Shub-Nigurath
12- Agents of Cthulu
13- Bishops Thralls
14- Beast Thralls
15- Naomi's Crew
16- Sorcery
17- Whipporwils
18- Bad Luck
19- The Beyond
20- Hideus Abominatios
21- Delusions
22- Byahkee
23- Inhabitants of Carcosa
24- Evil Portents
25- Hauntings
26- Hasturs Gift
27- Cult of the yellow sign
28- Decay and Filth
29- Midnight Masks (Only the 5 treacheries).

For some truly strange challenges, add the following encounter sets to the list.

30- The Gathering (Only the three Enemy cards)
31- The Miskatonic Museum (Void rules apply, shadow spawned starts in play)
32- Essex Country Express.
33- Blood on the altar (Do not gather Silas Bishop nor Kidnapped!)
34- Where Doom Awaits.
35- A Phantom of Truth (Twin Suns Places doom rather then removing it.)
36- The Pallid Mask (Do not gather humanoid enemies)
37- Black Stars Rise.

I recommend using the D66 version blow, it's a little more straightforward and has the potential to double up!

The D66 version.
1- Curses!
-1 Anchient Evils.
-2 Decay and Filth.
-3 Chilling cold.
-4 Locked Doors.
-5 the Beyond.
-6 Sorcery
2- Monsters!
-1 Agents of Shub-Nigurath.
-2 Nightgaunts
-3 Inhabitants of Carcosa.
-4 Ghouls.
-5 Beast Thralls.
-6 Hideus Abominations.
3- Madmen!
-1 Dark Cult.
-2 Cult of the yellow Sign.
-3 Bishop's Thralls.
-4 Hasturs Gift.
-5 Naomi's Crew.
-6 Delusions.
4- Madness!
-1 Striking Fear.
-2 Hauntings.
-3 Agents of Yog'sothoth.
-4 Agents of Cthulu.
-5 Agents of Hastur
-6 Whippoorwils
5- Lies and Hindrances!
-1 Midnight Masks.
-2 Bad Luck.
-3 Evil Portents.
-4 Rats.
-5 Byahkee.
-6 Roll a D8 and add 29 to the result, gather the appropriately numbered encounter set above.
6-Double!
Roll Two more times on this table, re-roll any result that would trigger more rolls on this table. (Alternatively, to stay on the safe side, the participating players democratically decide upon and choose any one encounter set).

Disclaimer: Some encounter sets may absolutely break your game! Also, all rolls are final!

PS: A D66 is rolled by: Roll a D6, this is the range, then roll another D6, this is the specific result, in this system there are 36 possible different results. If you rolled on the table above, a roll of "2" is a "Monsters!" roll, and then a roll of 4 would mean you have to add Ghouls to your encounter deck.