Sorry its been a while since my last update, anyway.
I have the circuit working in the more important ways now, but there are still some things I'm confused about. Still in reference to the last schematic I posted;
I added a high pass filter between the op amps and that basically killed the DC offset. Although are still a few mV under... I tried to add a divider to the virtual ground on the second opp amp (nothing but a non inverting with gain), even with the simple 2 10k over 5v it didn't move the output signal. The voltage divider was pulled to the original voltage, any ideas? But I guess when it comes down to it a few mV doesn't matter, its just I would rather understand why and be in the positives for sure.
As I was adding all the high pass filters I put one on the final output, but this caused problems with the signal? Its probably not a big deal that I don't have this final filter, but I really don't see why its giving this result when it works fine from the first op amp stage (perfect diode with gain). I'm I crazy and its just a mix up in my circuitry, not that there is a lot I could get wrong for this.
My out put voltage seems to be hitting the roof at 0.6v, I'm not so confident I can just get around this in the software. Although the way I'm doing it with the 2D gain control as long as I know if the signal is in the range it should be ok? But again that's certainly not the best way to move forwards. The max of 0.6v is even when I'm using fixed resistors, so the digipots aren't the problem what is?
Thanks (if anyone is still following this a month later!)