J100 Pins 1 and 2 CLK90 Clock Source is Internal
Pins 2 and 3 CLK90 Clock Source is External
J104 Pins 1 and 2 CPU Clock Source is Internal
Pins 2 and 3 CPU Clock Source is External
external for 68040. so 2-3 on both J100/J104.
this is based on your statement : a3640 works fine in your other amigas.
Other than that, the socket is ok on the a4000T, but maybe the 3640 connector is worn? only qualified service man can fix that.