IN-Line fuse for alternator?

There's no fuse in the alternator cable. There is two fusible links at the distribution block, however. I haven't gotten around to replacing them on my car, so in the meantime, I'm running some 4 gauge welding cable that replaced the factory cable, since I had a persistent hard starting problem that was due to my battery always having a discharged state. I replaced every cable though. Had the engine out, so I tore into the harness and replaced the starter cable, ground, and relocated the battery to the trunk. I'm happy to report no more problems.
 
For what it's worth, you could probably replace the entire cable for under $15. Figure some ring connectors, solder, and cable can't be that expensive. I always prefer to go the route of soldering rather than crimping ring connectors, so here's a quote of a post I made in the past:

StangGT1995 said:
The best way to go IMO is to pick up some welding cable and ring terminals like these to make your own cables:
ringconnector.jpg


Heat the terminal with a torch, fill it with solder, and shove the wire in while the solder is still hot. Put some heat-shrink tubing over the connection, and you end up with something better than new, without having to crimp on a connector and risk a bad connection that has a lot of resistance.

Edit: had to fix the pic link and I forgot to quote myself...
 
If your battery is showing more than 12.6 volts with the car running, the fusible links in the charge cable should be ok. They are located on the side of the PS bracket (between the bracket and the underhood fusebox).

There is also a stator fuse in the underhood fusebox.

If it's deemed necessary, you can certainly make a new alternator charge cable. I did as Matt outlines and used 4 AWG stereo cable with an ANL fuse. The stock cable was dropping ~400mV and my new cable drops 2-5mV, Note that this is a side thing - it should not help your issue.

Good luck.