Yes on WinUAE there was not much diference between 040 and 060 (with the new version of WinUAE a little difference now there is)
I recommend the 060 because that way you can use all OS3 software and libraries, if you use an 040 the "native" 060 applications and libraries will not work.
You usually have them compiled for 040 also, I know because I went from vanilla to 040 to 060, I was used to get native libraries for each processor. Nowadays I don't even know if it makes sense all the hassle, I would have to see benchmarks.
There should be little difference, but the best configuration should be 68030 + 68882 because it's the one where ALL instructions (besides CALLM/RTM, which were never used) are "executed" and don't call the trap handler.
68040 and 68060 had missing instructions whom execution invokes the very slow trap handler, which requires the execution of more instructions even using the JIT.
This doesn't happen if you have binaries which are specifically compiled for 68040 or 68060, of course, because there'll never be missing instructions executed (compilers had care to avoid generating them).
P.S. 68040 introduced a new instruction, MOVE16 (also available on 68060), but it looks like that there were bugs on some processors which makes it better to avoid its usage.
