The speakers you have will exaggerate any small differences too and as I remember, weren't really geared for 'digital' sources unless they're perfectly behaved, so proceed with caution here to prevent lost fillings and/or bleeding ears Some amps with built in DACs (some Yamaha's I recall) have pretty dire sounding digital inputs and a sub £100 headphone/DAC type recommended here and there can 'sound' better fed to the analogue inputs. Only thing is for you to make some kind of plan and procedure for experiment and see if you can hear anything if you change things.
These days, I believe the differences between SPDIF, USB and optical digital inputs may well be more due to any shit coming down the electrical connections and whether the DAC can deal with this. Connecting a PC it has been recommended to use the optical connection to offer electrical isolation. My own shit here, I can't tell any meaningful difference between SPDIF and optical and my workroom PC is fed to the DAC via a USB cable and a USB-SPDIF converter that used to be available for twenty quid - sounds amazing to me, but your mileage may vary on this..
Good luck - try to be as methodical as possible but don't get anal about it. It's the music and NOT the sound when all's said and done