Thought it was clear that yes you notice an improvement in S/N just by going from mic input to line input and even better going S/PDIF in. The MixPre-D is an excellent preamp and compliments the PMD661 very well -->
http://taperssection.com/index.php?topic=149760.msg1997485#msg1997485 Noisy mics will be noisy no matter what you feed them into so if your mics are the source of the problem then a MixPre-D will not make it better.
For mic(s) with PMD661 start by setting attenuation to -18 (this is actually zero gain, all the other settings will add gain which also adds noise), raise it incrementally though if your mic(s) don't give you enough level set at -18.
I have a ME66/K6 combo, it can send out a real hot signal that approaches line level unless you use a K6RD powering unit when recording loud sources. Be aware "Brick walling" occurs when the output of your microphones is too hot for the preamp input. Basically the signal reaching the deck can be adjusted where you want but if the signal comes in distorted it will be distorted no matter how you adjust the recorder.
I'm using v2.03A, this version provides better card compatibility though I've had no issues with any of the previous versions.