EQ software

No, it can't apply different curve to each channels, but unfortunately I'm unaware of an VST EQ that can and has such good characteristics (especially the GUI). If someone knows something like that, I'm also very interested :)

I have not tried, but how about running linuxDSP , one for each channel?

Also VST equalizer plugin for alsa - perhaps runnning two in parallel, each with one channel of the incoming stereo stream and later having the two mono channels joined again. I have not tested either.
running foobar...looking for a decent EQ so that i can EQ my full range Fe127e open baffles.

Don't know if this is what you are looking for, but it is possible for example with the Room EQ Wizard to measure and EQ each channel (you can average also different listening position measurements), save the impulse response as wav-file and import it to foobar (convolver plug-in necessary).

Haven't tried it so far, but a nice feature.