One thing to remember is that the 68060 doesn't use a double clock for anything. A 25MHz 68040 is run from a 50MHz clock in 100% of the cases I've seen. A 50MHz 68060 is run from a 50MHz clock. There's one pin for bclk and one for pclk (unless my memory is wrong, I have looked at a 68k cpu for 2 years now), on the 040 these are different but 060 the same. I think :-)
Except for this there's a couple of odd differences I don't remember at the moment. Anyway, it is doable, because Motorola made 040-060 upgrade kits which only had a PGA to PGA converter with a voltage regulator on it. Everything else was done by rewiring...