How do I warm up my system?

What is your room like? Are the walls hard like panelling, or are they wall board. Do you have lots of glass picture frames, windows etc? Is the room void of furniture? Is the room square or rectangle? Do you have carpets, hardwood or, cement floors?
All of these are a good source of brightness, soften up the room for starters, read all you can about acoustics and room treatment/speaker placement.
Hope this helps.

Large room, tall cathedral ceilings, carpeted, large picture windows.

While you are awaiting a more comprehensive solution, please try the $7.95 Herbie's Audio Lab Grungebuster2 CD mat when you play CD's. For this microscopic price, the bright, harsh edge may be tamed enough to let you relax until other ideas can be considered for system/room tuning.
Herbie's proprietary isolation feet beneath your equipment and speakers may further help, again, very modestly priced, and returnable if not working for you.
The effect of absorbing micro and macro vibrations throughout a system can sometimes manifest as relief from what troubles you about the sound, as well as making other aspects of your sound get better. The extremely long 90 day trial period is enough time to be sure of what you hear, even as you make any changes suggested by other Audiogon members.

Dac or eq is not going to do. Get that sony as far away as possilbe and dont use it as at transport.use it to play background music outside.

Throw some Vibrapods underneath your cd player tha'll help big time...............