I am really enjoying this thread. It gets down to the nitty gritty of what refining is all about - setting up goals, experimenting, and then going with the best bet. I would think the goals should be such things as simplicity, speed, inexpensive set-up, small amount of waste, low chemical cost, and, most important, efficiency - you want to get essentially 100% of the gold. Also, there are questions such as what amount of fumes your setup will tolerate.
Sorry, I didn't notice that both sides had traces. Back to square one.
From your most recent figures, there are 5472 sq.in. of plated area on the 2-sided 125 sheets (100@12x21 and 25@12x12 - your figure of 24 sq.in. on one side of the 12x21 sheet comes out to about a 9.52% plated area). From all this, there are 86.5g Au, 558g Cu, and 80g Ni. The total of all three is 724.5g and the total of the Cu and Ni is 638g.
Theoretically, it would take 2.66 liters of 70% nitric to dissolve all of the Cu + Ni and it would take 3.02 liters of 4:1 AR to dissolve everything.
I still don't think that anyone knows the best way to run this stuff. We have come up with quite a few options. They would probably all work but some would work better than others.
The more I think about this, the more I think that the material is best left in sheet form and not shredded. I know that this will take more handling but, if you use nitric or HCl/H2O2 to dissolve the Cu/Ni, the loose foils would be easier to remove from the sheets than from the shredded material. If you used AR or HCl/bleach to dissolve everything, the sheets would be easier to rinse than shredded material.
It sounds like the HCl/H2O2 is sort of working for you in what you've done so far. One good thing about this solution is that it's cheap and, since it's only dissolving the Ni and Cu, you can use quite a bit of it.
How to run more than 1 sheet at a time - thinking out loud department. What if you had a 5 gallon bucket and a 3 gallon bucket (with maybe a dozen 1/2" holes drilled around the sides and 3 or 4 on the bottom), that fit inside of the 5 gal bucket? The sheets could be cut in half (into 6" x 21" pieces), a few plastic paper clips put every 3", or so, on the top, bottom, and end edges of each sheet to act as sort-of spacers, and then the sheets could be curved around the inside of the inner bucket - it shouldn't make much difference if they overlap on the ends. You could probably put quite a few sheets in there at one time. The inner bucket should have a plastic handle so it wouldn't get eaten by the acid. You could normally keep a lid on it and then, occasionally, lift the inner bucket up (slowly!) to drain and then put it back it. As you brought the bucket in and out several times, you would surely get solution flow between each sheet and agitation always improves the reaction rate. The only thing making the sheets stick together is surface tension. This would be broken easily, I would think, by the solution flow. I would imagine the plastic paper clips are PE (same as the buckets) and wouldn't be affected by the acid. It would probably take about 3 gal of acid to cover the sheets.
I would suggest trying this on a very small scale using smaller strips of material. Just use a couple of small plastic containers. I would first try HCl/H2O2. If that works, you may be home free.
This could be done with nitric or HCl/H2O2. If using nitric, I would set the outer bucket in a plastic tray in case of foamovers. I would think that nitric would be much faster.
All of this assumes that the acid will penetrate through the gold and will dissolve 100% of the Ni/Cu. If it doesn't, you will probably have to consider dissolving all of the metal with AR or HCl/bleach.
I would bet that lazersteve has some suggestions on how to best use the HCl/H2O2 in this application.
OR, maybe you could just use two gallons of AR in the outer bucket and cut the sheets in thirds (4"), the long way, using the same 2-bucket/paper clip system as above. I would think this would be the fastest way, by far. Also, you wouldn't have to screw with collecting the foils. As Oz said, use only enough nitric as necessary and you won't have to evaporate.