It's no clear what you mean by "I had to change the STK", but if that means you have somehow defeated the fusing or place a larger fuse than it requires then STOP and shut it off. You might be risking a fire or more serious damage to the amp.
I would recommend you find a hands-on tech to look at it.
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If you have resolved the fuse problem and now just have low subwoofer volume, you might want to track it back to the source and ITS subwoofer volume setting. There IS a volume level control on the sub, too. Turn it up.
The manual is here:
http://www.retrevo.com/support/Sony-SA-WM500-Subwoofers-manual/id/752ag404/t/2/
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