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Acoustic Bass Pickup Volume

I recently did a trade for a Michael Kelly Dragonfly. I was told there was a repair done to try and remedy a buzzing E string. The owner was unsure of the extent of the repair. He did complain that the pickup did not have a consistent volume between each string after the repair.

The guitar has a intonation issue and the action is/was way too high. At first glance I thought it was just a truss rod adjustment. After doing a slight rod adjustment the intonation got better but it is still a good bit off on the A and E string. Later, while restringing I pulled out the saddle and realized that a wedge of bone had been glued to the bottom.

The A string is noticeably more quite than the E string when plugged in. I'm not familiar with acoustic pickups so I assume the pickup is located in the bridge. Does string distance from the pickup effect the volume like an electric pickup?

Would taking a belt sander to the bottom of the saddle be a bad idea?
 
It is imperative that the bottom of the pickup and the bottom of the bridge slot are dead flat. A buzz is remedied by raising the saddle.

It is very possible that someone placed a small shim under the E string portion of the saddle. That would create a large (this is relative, but thousandths count in a major way.) gap under the A string, less under the D and more or less contact under the G. It is that lack of contact that will cause a weak response on the A string. Take the strings off the tuners and carefully lift the saddle out of the slot to determine if this is the problem.
 
Yeah I'm not a huge fan of the ABG but since separating from the wife and moving back into a apartment it has been great for quite late night playing.

I would still like for it to be playable when plugged in. I guess the worst I could do is mess up the saddle and have to buy a new one.

Thanks for the bit of info.