"After a half a day, I hooked it up and the sound was incredibly poor. Very hard sounding, harsh mids and highs, narrow soundstage, no impact to bass, no definition."
That's a pretty damning review of a piece of high-end gear, warmed up or not, and would make me wonder if your unit may have a fault. A few days break-in certainly helps, especially with mechanical devices (speakers, CD transports), but 1000 hours? That's 42 days straight running 24/7, and doesn't sound right to me.
I only have a fairly budget system (Denon DVD1920 source, NAD c320 amp and B&W 602's), but could never describe it's sound as harshly as you have yours; I'd be looking for some other reason than break-in as your problem.