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I measured the voltage at the collector and it was above 6V. That voltage should be about half of the supply V, right?No! For one output (the usual amplifier), lightly loaded, half is a good start. So with -two- outputs, 1/4 3/4 is a similar good start.
With load, the transistor will pull "in" real well but the resistors pull out not so well. 30%/70% even 33%/66% may be better.
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should I bias the transistors differently for a 9v power supply? ..makes my brain hurt. 
How does this bias *work*? Ratio of base resistor, divided by hFE, to load resistors. This much will work the same at ANY supply voltage. There is also a Vbe in there, but if supply is >>Vbe then we can ignore it. 9V is not SO much greater than 0.6V, but we can still turn a blind eye to it. The variation in hFE from one part to another is greater.
And if you would use the intended 20V supply, it would not matter, because signal level is much-much less than supply. (In this case, I know that, because the LDRs will distort for >1V signal.) You could bias at 3V and 17V, or 7V and 13V, and signal would pass clean. Yes, at 9V you may have to take care with bias.
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Is there a more hands on approach to biasing transistors? like, using a breadboard and multimeter? Crank the biggest signal you expect into it. 'Scope the works. Is it clipping? Which side? Adjust Rb for less clipping. If that can't fix it, reduce "the biggest signal you expect" until it works, or drowns in hiss (unlikely).