I can't answer your question... I haven't looked at the code so I don't know how the sample rate is set... But in general, lower sample rates are "easier". There is less data to process and it frees-up the processor to do more stuff.
ideally i would like to lower it from the 39.somethingkhz down to 1000hz continuously.
Are you sure about that? Are you familiar with [u]Nyquist[/u]. ...Basically, you have to sample the top-half of the "wave" at least once per cycle and the bottom once per cycle, so with a 1khz sample rate, the maximum audio frequency would be 500Hz. That doesn't cover the range of your guitar, even before considering harmonics... It's not even good enough for voice![/b] (The traditional telephone sample rate it 8kHz.)
And, you have to low-pass filter before sampling, or you'll get [u]Aliasing[/u] (false "non-musical" frequencies).