@Jose:
As you should get somewhere around 18-19 MIPS in Sysinfo with the A3640 I have some questions:
Do you have the standard 68040.library in LIBS:?
Are both the J100 and J104 jumpers on the motherboard set to the "EXT" position?
Is the crystal on the A3640 a 50MHz one?
(edit): One last thing - did you have any working fastram on the motherboard when you got 14 MIPS in Sysinfo?
/Patrik