I am mostly sure its only a jumper on the motherboard. Its been a long time, but they are on the big book of amiga hardware data base. Changing the CPU is something I can do but finding the correct one now is nearly impossible. I only see PGA packages from macs and imbedded system floating around. I honestly don't see why you would need it done if you are using a CPU card though. Just change the jumpers from 16 to 25 mode I believe. Also this thread may help:
http://eab.abime.net/showthread.php?p=1098682Try moving J100 as if you had a 25Mhz and see what happens.
From CS MK2 manual:
Appendix A 'Jumper configurations in the amiga 3000 and amiga 3000t'
"The correct jumper position for the operation of the cyberstorm MK2 for models amiga 3000 and amiga 3000t is according to the basic positions as given in the corresponding computer user manuals.
It is only necessary to check the jumper position in case a different turbo board had been installed before the installation of the cyberstorm mk2"
From the A3000 manual:
Defaults for a 16mhz A3000 (313311-01/-02 (PAL/NTSC) in the jumpers table)
J100 2-3 Quad clock source (Positions: 25/16/ext)
J101 2-3 FPU clock source (Positions: ext/int)
J102 2-3 System clock source (Positions: ext/int)
J103 3-4 FPU CS/BERR (Positions: off/berr/on)
J104 1-2 CPU clock source (Positions: int/ext)