I know you said the drums sound okay when played through the keyboard's speakers, but have you tried changing the Accompaniment Volume (page 37) or Part Settings (page 74)?
Other than that, I'm wondering if anything might have happened when the USB was installed in place of the floppy drive. Do you know if everything sounded okay over the headphones before that was done?
If you were able to install the USB yourself, perhaps the service manual would help you diagnose and correct the issue? You can download the service manual from Elektro Tanya:
http://elektrotanya.com/yamaha_psr-550_sm_1.pdf/download.html
http://elektrotanya.com/yamaha_psr-550_sm_2.pdf/download.html
There are two different files, but I don't know what the differences are, so I'd download both versions.
Note that when you first navigate to each of the above pages, you'll need to wait patiently for a minute or longer until the "Get Manual" link appears below the picture. You do
not want to click on any "Download" button that might appear on the page, as it will actually be part of some advertised product that has nothing to do with the service manual. Instead, click on the "Get Manual" link when it finally appears.