Clickboom 060 quake is 20-30% faster than with my 040 40mhz, should it be faster? Difference is like mhz vs. mhz? 40mhz vs. 66 mhz
The 68060 should be about 1.7x faster than the 68040 at the same clockspeed in general use. So, assuming your 060 is 50MHz, generally you should be getting 2x the performance of your 040.
However, the actual speedup you get is very much dependent on the nature of the task. If you are playing Quake on AGA then you hit a bottleneck. Writing to chip ram is pretty slow.
However, if things are generally slow it may be the case that some frequently called bit of code hasn't been mapped into fast ram. I had this issue with my very first 040 board (an apollo 1240). RemApollo fixed that, perhaps you could check BlizzKick?