I don't understand why the -55 part would be considered a problem? That rating is the max in-spec speed rating of the 2Q_X clock line out of the chip, and I don't think that is the clock that's driving the CPU is it? I thought I saw in the datasheet that the 2Q_X clock is specifically not suitable for driving the clock of the 68040. I'd imagine that Q1, Q2, or Q3 are used to drive the CPU, and those are running at 44 and 45 Mhz in your case, which seems fine? Though anything running off the 2Q_X in your setup would probably have a very unstable clock.