Well I guess I'd give it some time to settle in. Whenever you first look at a new purchase you're bound to be overly critical of the car, and your purchase. Don't beat yourself up, just take some time to give it a good look, and then address each item as you find it. I wouldn't totally rewire the car unless you find things aree much worse than a few connections. I'm not sure what the inline fuse at the firewall is hooked to? If it's the main feed to the fuse block, then it should have had a fusible link down at the starter, and someone may have put in a new wire and the fuse to protect the main feed. If so, then I'd get a new fusible link and replace the wire from the starter up to that point to eliminate the fuse.
You lean something new everyday. As mentioned earlyer. But hey its a older car it better wiring than some dry rot or something crazy like that. But its a hobby these (old cars) just dont beat yourself down to much. Just lesson are learned everyday. And thank God you find this issue and not have a fire hazard on the freway or something. Just simply fix the issue and enjoy the vehicle.
I think it's: You paid for what you got. Check battery voltage. If it is below 12.3 or so, charge battery. Get yourself an open barrel crimper and if that connector fits the alternator, crimp it properly, bend the tab that holds it in the insulator back up, push it back in the insulator, and reinstall on the alternator. Fire it up and take a voltage reading at the connector to make sure the alternator is charging. Check battery voltage tomorrow. If it is below 12.3v or so, you have a drain or bad battery. Auto stores will load check batteries for free. If the battery is good and you need to inspect under dash, do yourself a favor, and remove the seat (as posted above). Check the inline fuse and figure out what it powers (bet it is a relay near front somewhere) for future reference. If you decide to keep that in line fuse, they have covered and waterproof versions.
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