[quote name='Tankdave' timestamp='1343325221' post='1749038']
Some of the noise is cool, it proves a real bass is being played and not just some synth or sampled stuff.
[/quote]
This - I've had some recording jobs where we've deliberately gone for a 'clanky' sound. Congratulations, you've nailed this technique, now that you feel it's time to move onto another approach I'd echo what's been said on here already - flats and cut the top of your EQ.
The disadvantage to playing semi-acoustic bass guitars is that the pickup is invariably a piezo mounted under the bridge - the place of least bass and most top. That is going to be a major factor in the amount of squeaks and such, so don't beat yourself up about it too much.
Altering your RH technique is something that I had to consider when I was playing my SA bass; it took a while, but I got there in the end.
Oh, that and I removed the frets - got rid of the fret noise, see?