It is a common misconception that the B+ wire from the alternator to the battery should be fused near the alternator. This is incorrect.Is the red wire going to the alternator fused near the alternator? Was the start battery switch ON? Is the alternator output wired directly to the batteries or does it go through the Start battery switch?
I would determine if it's possible that the positive alternator post contacted the engine....
Engine was a 4JH? ?
The output from the alternator cannot exceed the max specified output of the alternator and the wire should be properly sized for that current so there is no need for a fuse near the alternator.
The fuse is to protect the wire from a short to the battery which can easily exceed the ampacity of any wire and should be as close as possible to the battery. It does not protect the wire from current output of the alternator. On my boat with 560Ah of LFP battery, I have a Class-T within 6" of the battery positive terminal. I then have another 200A MRBF fuse where the alternator wire connects to the positive charge buss. The MRBF is probably not needed but it predated the LFP and Class-T