Cheats from Project64 Cheats Board.
I don't know about any specific MQ problems but those dungeon "problems" you listed aren't problems at all.
I think the settings will need a bit of tweaking to run this one 100% properly. Certain speed-hacks might need to be disabled...
As for the GFX, they should work exactly the same as the OoT GFX. There is no difference in this regard. It's still an N64 ROM - any porting issues have not yet arisen and it should still be the standard OoT GFX engine (and I don't believe there are any new GFX for MQ)
Legend of Zelda: OoT Master Quest
Also, here's the one of the original RDB entries for experienced users to take a look at:
[1D4136F3-AF63EEA9-C:45]
Good Name=Legend of Zelda, The - Ocarina of Time - Master Quest (U)
Internal Name=ZELDA MASTER QUEST
RDRAM Size=4
Counter Factor=1
Save Type=First Save Type
CPU Type=Recompiler
Self-modifying code Method=Check Memory Advance
Reg Cache=Yes
Use TLB=No
Use Large Buffer=No
Linking=Global
Status=Playable!
Core Note=
Plugin Note=
Delay SI=No
SP Hack=No
Clear Frame=0
Self Texture=1
Primary Frame Buffer=0
Resolution Width=-1
Resolution Height=-1
Culling=1
Emulate Clear=1