I am staring at this very problem on my 1965 390 powered T Bird.
When I first got the new motor and wiring all hooked up, the girl would'nt turn over. The Neutral safety switch (I didn't know what it was at the time) on the firewall would click.
The friend that was helping me said that I probably had the I (ignition Brown) and S (start Red/Blue) wires mixed up on the starter relay.
After switching them the Bird would turn over with the key on. Then with a clunk the battery died... for good. I had to replace the brand new battery completely.
I then replaced the starter relay thinking that was the problem. Now it starts as soon as the positive cable is hooked up.
After looking at this thread, I'm thinking the neutral safety switch on the firewall has been cooked by me switching the wires.
I have been double and triple checking the alternator and other wires to be sure before I continue. My guess is still the neutral safety switch.
I will update this thread as soon as I have it figured out, I hope this may have helped direct your search.
If you get some answers, please post them here and I'll check in tomorrow.
Good hunting.
Jer
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