You could try running the Wadia through the ML. I know all things being equal the less you run a signal through the better but...
Many people find the if you CD player has a digital variable output, it sounds best when they have the CD player set to full and then use the preamp to adjust the volume. Reason being is your CD player operates the volume in the digital domain and by boosting the volume there all your preamp has to do is resist part of the signal, (no gain required) letting more nuances and fine details in the music through.
My best friend has a Wadia 6 and he finds this true with his. In the review on the Linn Genki by UHF I believe they said that the variables output were so bad they could not believe that Linn even put the on (not bashing the Linn, it's a very nice player and I would like to get one, but those variable outputs are awful).
In the end of course it is your ears that must be happy so choose whatever you think sounds better, but it just and idea.
As far as other advice, you never mentioned your cabling, inter-connect, power, speaker... Asuming all of that is up to par with the rest of your system you could look into power conditioning.
It WILL make a world worth of difference. There are many threads on them in the archives, but if you got the money try a Hydra or PS Audio (The hydra is passive (filters) while PS Audio is active (regenerates) ). If you don't have that much you could consider a Monster Power Center (what I end up buying on a limited budget) or a Chang Lightspeed. These are by no means the only good brands out there. There are many more, these are just a few companies I have had good experinces with.
Other than that, nice system and happy listening.
Cheers,
Nick
