Don't do that! That's probably the code it's using to detect the slow code. If you patch it, it might not find what it's looking for to patch. There are some other types of critical code that should not be patched too. Patching some of the P96 libraries (and probably CGFX) for example will not work because there are a lot of exec/SetFunction() calls. You don't want to patch the 68060.library or SetPatch for obvious reasons also.
Ok, I was just playing around with it just to see how it worked. Haven't used it on anything important yet. I took a look at the code to try and understand it a bit more but my 68k assembly is as fluent as my Swahili.

From me? Probably not. I've thought about making an automated optimizer but the code really needs to be disassembled correctly first to make a lot of changes. I have worked on a new version of ADis which does a pretty good job but needs more works and I've been involved with other projects recently. It would still never be completely safe to do an automated disassemble, patch and assemble but it could be pretty good and give disassembly warnings. It's better to focus on getting compilers to generate better code.
Please keep doing what you are doing. It's very much appreciated!
Don Aden's a good guy and knows what he's doing. A faster transfer speed should give a speedup. I have a CSMK3 68060@75MHz with a 15k UltraSCSI hard drive that gives a sustained 30MB/s, PFS, PeterK's icon.library and Voodoo 4 and there really isn't much delay on large directory listings B).
I've got an ACard IDE to SCSI adapter for my CSMK2 with an SDHC attatched to it but my A3000 is currently in pieces (with a PIV,a Deneb and a few other bits too) until i get some free time to put it back together, but I've got a nicely configured UAE setup that I keep tweaking until i rebuild the A3000 and can transfer it across.