@dougal
Well done, I hope it's all working fine for you. Can't tell what the residue is on yours, but my Blizzard 1260 has had a small amount of residue around the CPU pins since new (about 10 years) with no problems. Most probably leftover flux from the manufacturing process. Anyway, the differences are that the 68040 isn't actually 100% compatible with the 68030, as some functions have changed or have been removed - especially in the FPU. To compensate for this, there's a 68040.library which you need to have installed if you don't already have it, so most software will work fine once this is in place. It's just something to be aware of really, in case you find some software which crashes but worked before on the 68030.
As for overclocking: I wouldn't do it. The 68040 is already a pretty hot chip (the hottest of the 68k range) so clocking it any higher is only asking for trouble...