Aaron, You need to switch inputs to either the tape in or aux input. The CD input has a pair of resistors in the signal path that roll the highs somewhat and are not as transparent. I personally use the tape in which appears to be a direct path. There is an appreciable difference in sound quality.
As for tubes, give Art Ferris a call. He sent me a pair of very nice sounding Sovtec's that are quiet and extremely transparent. Also, a pair of 6H23 Russian tubes from Kevin at Upscale Audio sounded extremely nice. Look on the Audible Illusions site under technical questions. Art discusses tube brands and their effect on the Modulus's sound. You also need to replace the tubes about every year if you use the pre a good bit. The usual first signs are a roll off in highs with a perceived lack in resolution and transparency with, usually, an increase in tube rush.
Lastly, if you haven't, flip the four dip switches inside the preamp to take the capacitors out of the circuit. This firms up the bass and adds to the resolution.
I'm currently uses a 01 model and have ordered a new L-2 linestage with remote. It is reported to be the best yet---we'll see. Hope this helps. Feel free to e-mail me if you have any other questions you feel I might can help you with. Phil