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.
With the Mu 68060.library I use this line in my S:Startup-Sequence
MuFastZero MOVESSP ON
This makes the Mu 68060.library a little faster (instead of a little slower) than most other 68060 libraries. It is less compatible with a few very old programs.
I also built the exec v44.1 but it only comes as a 3.1 complete rom image (which you can't seem to split for some reason), this is no good for me because I'm running RemapApollo with 3.9 and patching the built in 3.1 rom image with the Boing bag updates (loaded as modules). I'm not even sure if it's such a great idea to run v44.1 exec.library if you are running 3.9.
Piru's exec.library is missing some functions that are necessary for AmigaOS 3.9.
I updated my CopyMem 060 patches to the faster version listed in this thread. This didn't effect the frame-rate in Quake though, even running without any memory copy patches doesn't seem to have any real-world effect?
CopyMem060 isn't much faster than CMQ060. The only time the speed difference might be noticeable would be a lot of small copies in a short amount of time. You do save a little memory over CMQ060. The patch is worth running on a 68060 over the AmigaOS 3.9 copy functions. If you want to "see" the difference, scroll around in a newer version of AWeb with and without CopyMem060 installed

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If you have a Warp3D compatible gfx card, let me know. I have some patches that will speed up GLQuake by a few frames. You might try MuRedox/OxyPatcher with other Quakes and see if it's any faster.