From what I read, it won't ask you to update to 3.6 if you delete the game data. If you go to the game data utility (under games in the PS3 XMB) you can delete it here to get rid of the 1.04 update.
Then once done, the next time you play just decline the game update and start the game normally... worth a try anyway! 
Also below is a MK Komplete Edition fix by brunolee:
I created 2 patches, "BLUS" and "BLES" if they have the MK9 and wish to continue with it, to not give conflict with another one.- For those who have the MK9 BLUS: Download the "MK Komplete Edition BLES"
- For those who have the MK9 BLES: Download the "MK Komplete Edition BLUS"
- For those who have no MK9 (or will use only the MK Komplete Edition): Download the "MK Komplete Edition BLUS"
INSTRUCTIONS:
After the download, and extracted the rar... In the folder "PS3_GAME" are files that replace the game (overwriting the files as they wish, on your PC, FTP, mutiMAN (MMOs)) Then just install PKG "MK Komplete Edition PATCH (BL **)" (placing the PKG on root in a pen with "FAT32 File System" and install through the ★ Install package files in the XMB)
MK Komplete Edition BLUS
http://www.mediafire.com/?7r64foxzvr6ad34
MK Komplete Edition BLES
http://www.mediafire.com/?tcrc7yd4ca558fx- Contains the cover of the game to put on multiMAN
- The version BLES of the game does not give in Portuguese, this in Portugal, in Brazil I do not know (MK9 with the same version also did not)
- I used the "EBOOTS's" changed by Scorpion2k7 used in the patches 1.2, 1.3 and 1.5).
Note: This is a FIX 3.41/3.55 for Mortal_Kombat_Komplete_Edition_EUR_PS3-HR release.
I put kodes for Mortal Kombat Komplete Edition (BLUS and BLES) in "Code Unique 2.3" by Octo (oct0xor)Only one problem, you stay with 2 Quan Chi in the game (for this does not happen just delete the folder "QUAN_CYBER" on pkg, and complete story mode to unlock QuanChi and CyberSub-Zero normally)
Unlock all costumes BLUS30902: http://www.putlocker.com/file/11DFCF52F9334C93 / http://rghost.net/39978906
Unlock all costumes BLES01508: http://www.putlocker.com/file/6D218171BAD81B5B / http://rghost.net/39978905
This does not unlock Skarlet and Freddy in Nekropolis. (complete story mode, or using the saves of old MK9 with it already done)
Non Playable Characters Finally Playable in All MK9 Modes by Tetzrep (via psx-scene.com/forums/content/non-2541/)
Download: http://www.mediafire.com/?h5r71vz7w9c7dlo (Password: tetzrep)
Please note: For the NPC's to properly work, you must at least be on version 1.02 of the game (this is the version that PS3UserCheat has codes for)
Unfortunately, the only way this is possible is to be on CFW 3.55 as we don't have a 1.02 patch that was ever coded for 3.41
and, as mentioned, this is the version ps3usercheat requires.
A Quick Guide..
Install PS3UserCheat .pkg on your PS3
Transfer the "st.dat" file to hdd0/game/CHET20000/USRDIR on your PS3.
Load the game in MM or whichever manager you use
Enable the cheats in PS3UserCheat
Press Load
This will probably kick you back to the XMB
Start the game..
BUTTON CONFIG
Code:
NPC_FIX SELECT
NPC_CLASSICJADE SELECT+CROSS
NPC_CLASSICNOOB SELECT+CIRCLE
NPC_CLASSICREPTILE SELECT+TRIANGLE
NPC_CLASSICSMOKE SELECT+SQUARE
NPC_CYBERNINJA_LK4D4 SELECT+L1+CROSS
NPC_BASEMALE SELECT+L1+CIRCLE
NPC_GENERICFIGHTERA SELECT+L1+TRIANGLE
NPC_GENERICFIGHTERB SELECT+L1+ SQUARE
NPC_GL_ONI SELECT+L1+R1+CROSS
NPC_JC_DIRECTOR SELECT+L1+R1+CIRCLE
NPC_TARKATANSOLDIERA SELECT+L1+R1+TRIANGLE
NPC_ZOMBIE_MALE SELECT+L1+R1+SQUARE
WHEN TO PRESS BUTTONS (button combo)
After difficulty select in Ladder or Test your Luck
During the ladder screen (not before)
After P2 select in Practice or Fatality Trainning.
After BIOs select in netropilis
WHEN TO APPLY NPC FIX (SELECT button)
After loadscreen has finished
During Intros
during rounds
during fatality
(ladder screen comes next)
(if you still haven't pressed Select by now, its to late.)
NPC FIX CHEAT
Must be enabled with NPC character cheats.
Because none of the npc charcters have images to support the ladder screen with, the game crashes and freezes up.
The NPC Fix cheat just defaults the P1 character to Scorpion, that gets it past the ladder screens. You then have the choice to re-enter the npc button combo or pick from any of them as you like.
BUTTON ACTIVATION COMBOS
The timing of when to enter the button combo is a bit tricky at first.
But the more familair you get with the load screens the easier it should get.
It must be entered after the ladder screen apears, but before the load screen starts processing. There is loading screen before every
match and its posible to change button combos before each time it shows.. pressing, holding or tapping the buttons all seemed to work fine.
High-Definition Boss ICON Fix by Tetzrep (via psx-scene.com/forums/content/high-2650/)
Original Boss Fix + Mileena Toilet Paper Costume and pack 3, 4
Only Install FIXBOSSCOPION2K7.pkg if you not yet Have the boss fix Install yet?
PKG File: Updated High-Def BOSS ICON Fix
Here is the Boss mod fix for MK9 update versions over 1.01. I put a readme in it for all versions too.
Manually: MK9 v1.02-5 HD Boss Game File's Fix
From: SCOPION2K7 Providing all of Us the actual PKG Boss Fix to play as the Bosses,
To: oubgrdevvbuyn Providing all of Us The 1st HD Boss Icon Fix,
Now Thanks To: Tetzrep. He have brought Us all a New UP-TO-DATE ((High-Definition)) Boss ICON Fix
Code:
Further Manually Info From Tetzrep
All mk9 versions over 1.01 will have to apply the usual fix. here's the ps3toc to use for it. PS3TOC.TXT
You can get the other files by unPKG'ing the download or by copying them from the install location here: (install the HDbossmod .pkg first) hdd0/game/bles01132/usrdir/dlc/bosses or hdd0/game/blus30522/usrdir/dlc/bosses
To apply the fix, go to actual game backup directory and replace the original files off the disc. (backup all original files before you overwrite them!) PS3 - hdd/games/Mortal Kombat 9/ or PS3 - usb/games/Mortal Kombat 9/
....usrdir/ - PS3TOC.TXT
....usrdir/asset/ - UI_PS_VS_JPEGS_PS3.XXX
....usrdir/asset/ - UI_PS_VS_PS3_N.XXX
....usrdir/asset/ - UI_PS_VS_PS3.XXX
If it still wont work, delete these files found in the ps3 cache. PS3 - hdd/game/blus30522/ or PS3 - usb/game/blus30522
....usrdir/ - PS3TOC.TXT & .time file
....usrdir/asset/ - UI_PS_VS_JPEGS_PS3.XXX & .time file
....usrdir/asset/ - UI_PS_VS_PS3_N.XXX & .time file
....usrdir/asset/ - UI_PS_VS_PS3.XXX & .time file
I think theres a video tutorial on how to do it somewhere too, I havent seen it though. hope yous get it working. The image change makes me want to choose them more now!.
The new HD bossmod .pkg should orverwrite the old one....
Note: Do Not add the PS3TOC File in the asset folder. Add it to the USRDIR Folder.
Update: Ultimate Mortal Kombat 9 (Komplete MOD Edtion + Challenge Tower Mods) Updated All In One character packs for Mortal Kombat 9 (via psx-scene.com/forums/content/tetzrep-2761/)
BLES01132
KME part 1 - DLC_Character_Content-BLES01132.part1.rar 180MB
KME part 2 - DLC_Character_Content-BLES01132.part2.rar 127MB
NPC cheats - NPC_Character_Cheats-BLES01132.rar
BLUS30522
KME part 1 - DLC_Character_Content-BLUS30522.part1.rar 180MB
KME part 2 - DLC_Character_Content-BLUS30522.part2.rar 127MB
NPC cheats - NPC_Character_Cheats-BLUS30522.rar
XBOX360
KME part 1 - DLC_Character_Content-XBOX360.part1.rar 180MB
KME part 2 - DLC_Character_Content-XBOX360.part2.rar 164MB
NPC cheats - NPC_Character_Cheats-XBOX360.rar