Standard CD is 44.1 kHz. DVD is 48 kHz.
Upsampling and oversampling is open to debate if it improves sonics.
Everyone has their own thoughts on what sounds best.
Some folks like the DIP, others hate it.
The stock SA-XR45 does sound very good. I feel it can sound quite a bit better when used with a Bybee Purifier in the digital cable.
If you are happy with your cable you can use this:

from
hereIf you would like to replace your cable, this is my choice to use

You can find digital cables with Bybees inside
hereBybees also tend to help the sound when used on the output of the amp or inputs to the speakers. Information about these products are
hereFinally about the best thing you can do to your SA-XR45 is to have it modded

You can have the Bybees installed inside and have most of the internal components upgraded. More information
here