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Electronic stuff (read MSD box, etc) does not like reversed polarity. You probably fried your electronic ignition assuming that is what you are running.
Did you turn the key "on" with the battery cables reversed? Did you try to crank the starter with the battery cables reversed?
A better description of what it is doing now would help. Even if you have fried the alternator, that would eventually result in the battery going down but it shouldn't prevent the engine from starting now if the battery is fully charged.
Wayne
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