Hi did this when changing my clucth in my 01 bugeye today but when i took it for a test spin the stereo dosnt sound the same. To be honest i never put system in previous owner did but it all looks right. Its nothing speceial but it was better than this before i disconnected the battery.
In short alpine flipdown headunit
twin basebox and amp in boot its supplied by good quality cabling .
When its turned up to 18-19 you can hear the speakers bottoming out!
Could disconecting the baterry do somthing like this maybe its gone back to factory settings. I never played with settings as it always sounded good how it was!!
Anyone!!

 

chances are the settings have reset

My battery went couple of days ago (same car) and now all my presets and settings have returned to default. Very annoying as it took months to get it right the first time.

Have them almost back now but you may need to have a play with the crossover points and equalizer settings on the head unit. From the sounds of it, you may need to adjust the bass frequencies more than any other if you say the speakers are at their max.