Usually the factory installs capacitors in high-noise places, like the blower motor, the distributor, etc. These are to keep the noise out of the radio power feed. If you blew one, it would explain the noise you're hearing now. You can try swapping them out for good ones, or install a line filter on the radio power input.
Usually noise in the speakers is caused from power running close to RCA cables or speaker wires. Sounds like your problem happened right after the jump-start, so I'd check the factory capacitors (a.k.a. noise suppressors).
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