Sorry to poor cold dishwater over this and I'm really not trying in the slighted to be patronising here BUT - you're using a plump-bassed VMS30 (I have one and have used it recently) in a rather soft toned arm (the SME III was totally opposite sonically to the 'Improved' series 2 that preceeded it - why do you think so many are being stripped out for spares?) on a deck that hints at greatness but never really gets there! I do know the deck you have and set up many many of them in my time and although the 'Super' was a subtle improvement on the base TD160 II, the mat change probably accounted for most of what you hear as a 'difference' and not the structural changes IME.
Apologies for appearing to diss your turntable system, but there's absolutely NO WAY you're going to get a neutral digital source to sound the same as it without loads of artificial software processing! It's the deck that's balancing a speaker-room situation I believe and the object should be to mellow the sound from the speakers out a bit, not slug the digits to match the turntable...
My advice is to use CD's for now and play around with speaker positioning, as well as absolute phase to get the DIGITS right, and then set about updating your vinyl system into something a little less coloured and turgid sounding. I know the truth can hurt, but I very much doubt I'm wrong in this particular instance, turntable wise at least.
Apologies again...
Tear down these walls; Cut the ties that held me
Crying out at the top of my voice; Tell me now if you can hear me