Thank you for the dry sample. the low pass really is a good thing. i didn't know it was that simple to add. did you you yet experiment with the capacitors values? you can simply add an euqualizer with a variable resistor before the capacitor!
i finally managed to built the smallest (yet quite powerful) possible amplifier yesterday, using a single darlingtion transistor (tip120) and 2 resistors. it was quite hard to figure out the right resistor values, but when they were set it was great fun to add and remove additional capacitors as their impact on the sound was quite big.
your absolutely right, concerning the PWM. it's not possible to generate tone frequencies using PWM. but it might be difficult using frequout together with midi-in. i think creating the frequencies is a very time-critical task. you'd have to be able to read the serial port in between the phases to get and interpret the midi messages... but i f you want to try i could help you with the general "midi-in" circuit and code. it's alpha, but does work reliably for me.
another idea would be to create the frequencies in a seperate circuit - that is controllable by PWM - to be able to use arduinos computing capabilities for more interesting stuff than switching one pin on and off. i'm not an electronics genius but i guess this should be possible. the second advantage would be to be able to mix multiple frquencies as we are not limited to one PWM.