Power Supply, Fuses, Wiring

Okay, I have a few questions.  I drive a 98 Honda Civic LX with a stock alternator. 

I have a fairly low-powered system which includes the following:Clarion DXZ535 HUMTX TA3202 at 4 ohms(50 watts) into Pioneer Rev 6.5s for the fronts.  My rear deck speakers are almost never used.Phoenix Gold Octane 5.0.1 at 4 ohms into JL 10w0 * 2 sealed cab.Stinger battery, Fosgate 1.0 Farad cap

Now I'm running 4 gauge wire from the battery to the capacitor, to a fused distribution block.  From the block I have 8 gauge running to both amps.  My main focus is SQ; I listen to more jazz, classical, blues, and early rock than rap/techno, although I do listen to some of that as well.  Is having the cap going to damage my alternator in the long run?  I did a search on caps, and that's all I'm reading, but there also seems to be a distinction between SQ and SPL users.  My biggest priority is clean, flat sound, but I want clean, crisp highs more than anything else.  I'm an electric violinist, and I want to hear every last detail when I'm listening to classical music, especially strings, piano, acoustic guitar, and cymbals.  I'm happy with the quality of bass I'm getting, so that's not as big a concern. 

I'm planning on using a 125 amp fuse at the battery, and two 80 amp fuses at the distribution block.  Will that protect my wiring and amps?  Am I using the right gauge wires?  Will the cap give me a cleaner power feed, or should I scrap it?  And finally, should I upgrade to a higher output alternator?  I honestly do not plan on further expanding my system in this car in the interests of practicality and trunk space. 

The fuses placed in the wiring paths are for protection of the wires, not the amps.  What you propose is fine because the fuses' values are not too high for the wire gauge used.   https://www.the12volt.com/info/recwirsz.asp Don't upgrade the alternator unless you have to.  When your system is installed and running you will know if the alt isn't putting out enough power.  If you already have the cap go ahead and install it if it makes you happy to have it.  I doubt it will be of any use though.Build the box so that it performs well in the worst case scenario and, in return, it will reward you at all times.