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I’ve got a similar project going, but I didn’t think to remove the USB and Ethernet jacks. I thought if I cut slots out for them that the Pi2 would fit, but the solder tips on the bottom of the PCB make it so I’m about 2-3mm too tight inside the SNES cart.
I wish they sold a Pi2 with single height USB jacks.
Any update on yours? I’d love to see the end result of how you got everything to fit.