Jason,
It's not your system that I think is anerobic.
It's your reactor.
If your whole tank was anerobic.. wow..
The smell woudl be summting else.
Since you used a pH monitor.. hmm
I'd say bump up the flow rate. I am running 75 ml/min with my reactor.
For flow rate that is. Once you start getting fresher water in there the smell will subside. As for the algae. I have seen that stuff before. It may go away witha higher flow.
Start at that rate and then adjust your CO2 accordingly to get the alk in your effluent that keeps up with your tanks demands.
I'd add more but I have to run.
Brad will chime in shortly I am sure.