Hm, hard to guess what could go wrong. Are you sure that the ICs are working fine? I've got one faulty CPU which fails hardware tests but runs certain demos. Maybe the CPU is detected by passing PHI2 but isn't doing anything else. Or one of the CIAs is faulty and can't access certain functions. Is it the same result when you swap the CIAs?
Using the terminal, have you tried to set all the functions in the menu 'M' to default? Should be a standard setting by default but perhaps it got changed.