I see you have decided to start with the aqua regia approach as the result of your heated discussion with your chemist friend.
Apparently the 13% Silver is too high to effect a complete dissolution and you do have encapsulated gold that has not dissolved. That gold is now coated with a dark green yellowish coating which is what the residue of gold alloy coated with Silver Chloride looks like when it is not completely rinsed.
The dark colored acid is from the copper as pointed out.
You will not, in the end when it is dried and melted, recover all of the gold. A percentage is tied up in chlorides and since you did not have the benefit of tumbling that percentage will be higher than it would be if you tumbled.
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For this experiment to convince you and your aqua regia inclined friend you should now take a sample of similar size, inquart it, and part it in nitric. You will then, with proper parting have >99% gold after rinsing which, when refined in aqua regia, will produce a nice red - orange acid after the reaction and will yield a very high purity gold.
Try the inquarting, you will come back completely converted to an inquart man. Then your chemist friend owes you a beer!