If there is a "hole" in one of the black "boxes", then you probably have found the source of your problem. The "boxes" are the output transistors for the individual amplifiers in your multichannel amp.
A "hole" is caused when the transistor die get so hot that it literally blows the plastic packaging material (the black stuff) out, leaving a little crater. The transistor probably got hot because it failed (shorted) internally, and so the +14.4 Volt supply got shorted to ground. This allows a buttload of current through the device, heating it up to the point that it blew out the packaging.
The failed transistor probably remains shorted, and this is why you are blowing fuses. Remove that transistor from the amp, or simply cut it's leads so that it has no electrical connection to the circuit.
New speakers, if they were of a lower impedance then the old speakers, may have caused the overheating of a weakened transistor.