Hiya,
Had a play with all of this last night.
Tried the MMU libs 060 (+mmu.library), seem to be stable but they also seemed to run Quake slower than than standard (patched) Apollo libs, also not sure how compatible it is with RemapApollo. I might still try to use them to create a 3.1 boot floppy to run some demos that don't seem to get on with my standard 3.9 setup.
I use this in my startup-sequence regarding the MuLib package:
MuMove4K PREPAREEMUL A1200
SetPatch QUIET
PatchRAM PORTPATCH
PoolMem INSTALL >NIL:
MuFastZero ON FASTEXEC MOVESSP=FASTSSP
MuFastRom
MuRedox
ConsoleFix
ConFix
The MuRedox part is equivalent to oxypatcher or cyberpatcher. I'm 3.1 though so I wouldn't know what 3.9 would need regarding the other stuff.
I'm sure I had better speed with MuLibs, or I wouldn't have used them. I may take another look at the Apollo library though being as though it's been updated recently.