Disclaimer: Electrical wiring can be somewhat complicated, possibly dangerous, so please be sure to fully understand what you are doing and why. When you design and install your own electrical, just know you do it at your sole risk and you own all the consequences (good and bad). You will find it very helpful to have a solid understanding of ohms law and how to safely use a digital volt ohm/meter for both AC and DC.
- order of placement of disconnect and fuse in the circuit (which one first in the circuit and why)
I wire a large battery main disconnect switch in the positive cable between the house batteries and the power distribution block. When the main switch is off, everything down the line is electrically dead. This is for service and also to prevent parasitic battery drain during storage. Individual circuit fuses generally go in the positive wire at the distribution block so everything down the wire is protected.
- recognition that fuses/breakers protect the cables, but what is a practical length to be concerned about? 6 inches seems pretty short
Breakers and fuses protect cables, switches, and the equipment. Even a very small unfused wire can pull tremendous amps to the point the copper glows, burns, and melts. Fuses are sized based on the anticipated equipment amperage needs plus a small safety overage. Generally, you want to use the smallest amp fuse that will get the job done. Wire size is related to the length of the run and amperage draw. Longer distances or higher amps need larger wire sizes to prevent voltage losses. There are wire sizing charts available online, but please note DC sizing is different than AC. Wires are sized by AWG (American Wire Gauge), a peculiar numbering system with larger numbers equating to smaller size wire (26 awg is tiny, and 0 awg is pretty big).
- idea that bus protection is different than cable protection - when a short occurs on the positive bus
If I understand correctly... when you say bus I'm assuming you mean you mean busbar or distribution block. For DC I fuse each house battery positive cable with a 150 amp mega fuse leading to the main disconnect switch, and a single cable goes from the switch to the distribution block. I do this in case one battery shorts so it doesn't affect the others. Smaller fuses go into the distribution block for individual circuits. For AC, the power cable from generator or shore power goes directly into the breaker box with a main breaker and several smaller circuit breakers.
- clearances between equipment - want to keep it small, but also need to be able to replace and work on equipment
Manufacturers can better advise on minimum clearances. Always keep heat, moisture, and vibration in mind when locating components. Consider what happens if there is a water leak. Wire insulation can chafe from friction, burn from excessive heat, or fracture internally from vibration or tension. Leave some wire slack, use drip loops, cable sleeve, fire sleeve, grommets, zip ties, etc. to keep things intact. I crimp, solder, and shrink wrap DC terminals.
- fuses versus breakers - a lot of the breakers on the market give me pause - thinking fuses/disconnects might be more reliable
I use breakers for AC circuits, and fuses for DC circuits. You can buy DC breakers but they are pricey and may react too slow so fuses are better for DC...