If you hooked a 12V neg alternator up to 12V pos ground you most likely destroyed the diodes in the rectifier system within the alternator.
The wire with the clip on it was most likely used to manually excite the alternator, a simple touch of the right terminal will start it charging and stay charging till it is shut down, next time the process has to be repeated.
Unless you can determine otherwise the alternator was probably neg ground as that is the standard, however they can be built for 12 V pos. or even 6 V applications. I would reverse the battery and try the system by running it and touching the regulator blade with the clip and see if it will charge, you may have to take it and get it tested.
If it is a Delco,they are very easy to wire an exciter circuit up to
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Today's Featured Article - Tractor Profile: Ferguson TO-20 - by Staff. When the infamous "Handshake Agreement" between Henry Ford and Harry Ferguson fell by the wayside (that's a story in itself), Harry Ferguson quickly set up manufacturing plants for a United States version of his English TE-20. The TO-20 was relatively the same as the TE-20 except utilized some different casting materials and had a US-style electrical system. The TO-20 was a dead ringer for the Ford 9N and 2N models and they say that Ferguson did this on purpose when the Handshake Agreement wen
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