General comments about using pickups with acoustic instruments.
Microphone pickup is typically fraught with the problems you describe, although it is theoretically the purest approach to amplifying acoustic instruments. With a good microphone, you can pick up the sum of all the sound from the instrument, albeit at a single point in space. Oh, and you have to be in a closed anechoic chamber to get it right.
The problems you are experiencing come into play whenever you bring the gain high enough to entertain a large audience at a satisfying sound pressure level. Basically, you are encouraging the electroacoustic feedback loop to be more active, to the point where it approaches and sustains the resonances you are familiar with and it completely changes the tone of the instrument.
The use of a pickup is probably the best approach to live amplification of instruments such as violin, guitar, cello, upright bass and so forth. At least the feedback loop can have a much higher acoustical gain before feedback. Now, the idea of amplifying the entire composite mechanical and acoustical sound of such a complicated instrument by a pickup of the vibration of one point on its surface sounds like an impossible proposal for purity of signal. However, we have found that some of these configurations do indeed present an acceptable illusion of total instrument sound, especially given some special care for tone shaping. To be clear on this, "acceptable illusion" is not a put-down. It is actually the best you can do. We are just starting to learn about this whole new world of amplification art, and we are fortunate to be doing it with some of the truly talented and dedicated leaders of the art.
The other way to amplify is to forget the original instrument and use a device that creates little or no acoustic sound of its own but rather an electrical signal that creates the illusion that the sound is coming from a traditional instrument. I'm talking about like what Ned Steinberger is doing. Of course, once you have the signal, you have to deliver the sound somehow. You have the ideal system for this, so keep the faith and stay tuned.
There you have it. I'd try a good pickup. We have a preset for a Fishman on a bass. These are very popular. The Realist is also excellent, but I've only heard this used on a bass, under one of the feet on the bridge. I'll ask David Gage tomorrow and report back. This is a new but expanding area of work for us.