A Mk2a should be fine -- the capacitor thing was for Mk2 units: removing a couple of caps from the PCB improved high end response, or something like that.

Scratchy sound is more likely to mean "bad connection", either in the docking connector, or the wires that connect that to the PCB, or perhaps a cracked trace on the PCB.

Since you said it happens only after things have warmed up, I'd bet more on the PCB.