If you were comfortable when doing that one pin, then I'd suggest hitting all the others now. The symptoms you are describing are 100% in line with a bad joint on the IDE header, and I have seen failing header joints that I couldn't spot visually. It really is worth eliminating this as a possibility before spending any more time chasing the problem down blind alleys, and the only way to do that is to retouch every pin.
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Mk2a 60GB Blue. Serial 030102962 sig.mp3: File Format not Valid.