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I know you probably have, but check your wiring again. Black boxes can be a result of one of the wires to the screen having a poor connection. I have a poor connection somewhere in mine and I get a line of black boxes if I drop it while it's plugged in.
What gauge wire did you use? If they're really small, I suppose it's possible that your poor connection lies not in your solder points but where you plug your wires into the arduino board.
As for uploading the code, you should be able to do it with a bare arduino board, you won't need the screen or wires to flash the ROM. I'll bring mine upstairs in a bit and see what it does when I flash it.
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