Hi Tom,
Thank you very much for answering my question. I will remove them with some sort of strainer. I didn't even think of that.
As for the beans, I purchased them from Chocolate Alchemy and had them roasted and winnowed. I know I am doing things backward but I am building a winnower and since I had the beans and the refiner, I wanted to experience what a finished bar would be like. I will study the comments on here and the forum on Chocolate Alchemy in regards to tips and reference points for roasting.
Thank you again!