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Regarding your preference to avoid putting the battery switch at the battery compartment:

The benefits of the 1-2-B at the house battery box make sense, but there is also a convenience to having it centrally located at the navigation station. It may be a sealed switch, but the back of the switch being exposed to fumes inside of battery box is a concern to me. I looked at nearby locations, but not happy with them. This is one of the reasons I spent time moving as many fuses out of the box as I could. Nothing is final yet.

I checked with BlueSea and they said it's fine so long as you avoid putting the switch directly over the batteries without any ventilation (note, their switches are well sealed, some lesser competing products may not be). Also, the ABYC standards call for the battery switch to be as close as possible to the batteries. I have communicated separately with MaineSail and suggested he weigh in for the benefit of the larger C34 community.

So long as there is decent access to see/replace them, I would probably keep the fuses in the battery compartment as well and use some protectant on the exposed surfaces. Moving them out is fine, too, but not at the expense of longer cable runs to them or reduced access.

Yes, Ken nailed it. It's true that Jon can eliminate the 150A alternator fuse since the wire is already protected by the 250A battery fuse. And, the battery fuse can indeed be 250A so long as entire path from the battery is always at least #1 wire rated at 90C or higher. (#1AWG @ 90C has an ampacity of 170A if passing thru engine spaces and using the 150% rule gets you just barely to 250A). Using wire with insulation rated at 105C would improve the safety margin and would be a good idea. I probably inadvertently contributed to Jon putting that fuse in, because at one point I told him that if he used an external regulator he could get by with less than #1 AWG to the alternator so long as it was appropriately fused at the battery end. That's what I did when designing my brother Noah's layout. Then when a fuse appeared at the alternator end in Jon's diagram I told him to move it back towards the battery, without noticing that it was unneeded due to the heavier wire used.

The Echo Charger indeed comes with a fuse at the end of each positive lead and that's sufficient if they are long enough. If you lengthen them you need to move the fuse to what becomes the new end of the wire, which is what Jon is now effectively doing.

As Jon noted, a "maintenance-free" sealed battery is typically still a flooded design, not AGM and probably has similar enough charging characteristics to work fine on the Echo Charger (and besides, the reserve battery rarely sees any use). Ken is right that a starting battery is a better choice for the reserve than a deep cycle and is also cheaper.  The expert on battery characteristics, though, is MaineSail and I defer totally to him.

Wire Ampacity table below:

It's shaping up nicely, with the physical locations shown, etc.  Couple of comments:
1. There should be a 20amp fuse in the wire from the Echo Charge to the Reserve battery within 7" of battery-end of the wire. The 250amp fuse at the battery won't protect the 12 gauge wire, and the one shown in the Settee is at the wrong end of the wire to do so. I would discard the fuse they provide with their 2' harness and add a 20amp fuse at the battery end. It can go on either side of the 250A fuse.

2. I don't see any electrical/performance issue with using a MRBF on the bus bar for the alternator wire, but since I have more theoretical than hands-on experience installing them I can't comment on any mounting tradeoffs compared to ANL fuse blocks. Maybe MaineSail will comment.

3. The bilge pump wiring shown is slightly inaccurate (for both pumps in different ways). For each there should be a single fused wire going to the on/off/auto switch and then two wires from there to the pump (one to its float-switch, the other direct to motor). Then, in addition, there is a negative from the pump back to ground.

4. It looks like you are leaving the 1-2-Both battery switch at the AC/DC Master Distribution Panel vs moving it to (or near) the battery box. Although the existing panel has a space for it, the advantages of moving it are several:
   a) Shorter cable lengths resulting in less voltage drop
   b) Easier routing of cables; eliminates heavy cables to/from that panel and in fact allows you to reuse the #4 that goes there today so that you don't need to pull any wires at all to/from the panel. The only heavy cables go to much easier destinations thru easier routes.
   c) Allows you to connect other loads such as the windlass to the C-terminal of the battery switch, solving your issue of the windlass running only from the house battery.

Paul,
Actually Ken is correct to be concerned about the max short-circuit current. While a simple view of a fuse is that it will fail long before that, reality is not so simple. When the instantaneous current is high enough, some fuses can fail in other catastrophic ways, such as arcing and/or exploding instead of simply opening.  AND circuit breakers can instantaneously weld closed from the massive flow of current and then fail to open. All fuses and circuit breakers have an "interrupting rating" (IR) or "breaking capacity"

https://en.wikipedia.org/wiki/Breaking_capacity
http://www.cooperindustries.com/content/dam/public/bussmann/Electrical/Resources/solution-center/technical_library/BUS_Ele_Tech_Lib_Interrupting_Rating.pdf

One cannot predict the maximum short circuit current from a battery by simply knowing its AH capacity. AH capacity relates to the total energy stored in the chemistry when consumed over a number of hours. Instantaneous short circuit current (if shorted right at the battery) is mostly a function of the battery's voltage divided by its internal resistance. The former is 12v, but the latter is rarely specified (small number of milliohms). The Cold-Cranking-Amps gives one some sense of the answer; the short circuit current is always much higher than the CCA. Once you connect to the battery via wires the max current is reduced due to the resistance of the wire between the battery and the location of the short. I suggest asking a licensed marine electrician (e.g. MaineSail) but in general fuses for protecting heavy gauge wires connected to batteries should have a "interrupt capacity" of at least 5,000 amps, preferably much higher. A BlueSea MRBF has an Interrupt capacity of 10,000A.
https://www.bluesea.com/products/5189/MRBF_Terminal_Fuse_-_250A

Jon,
Great work so far. I designed an electrical retrofit for my brother who owns a C34 in San Diego. In the process I engaged in lots of discussions with other forum members including MaineSail and Stu and am happy to share that.

Couple comments below:
Your #4 AWG wire from the alternator output to the House Battery busbar is undersized with regards to voltage drop for efficient battery charging if using an internally-regulated alternator. The output wire from an internally-regulated alternator has to meet a much tighter spec than other wiring. That is because even a small (0.3v) change in charging voltage significantly impacts charge time/efficiency.

It is extremely important that your alternator deliver the proper charging voltage all the way to the actual batteries. Any uncompensated-for drop will result in slow/undercharging of your batteries, which is the leading cause of premature failure.

There are two ways to address:

  1) Run sufficiently heavy wiring from the alternator to the batteries on both the positive and negative (ground) side so that the voltage delivered to the batteries is extremely close to what comes out of the alternator (within 0.2v). If your alternator outputs 80amps (sustained*) and the round-trip path is 20' (10' positive and 10' negative), then you would need to use #1 AWG wire to keep the total drop to 0.2v volts. Even that drop will reduce the bulk charge rate somewhat.

  2) Use a regulator that supports "External Sense" and run the necessary additional sense wire back to the House battery busbar. The sense wire can be very small gauge as it carries almost no current; it's just used by the regulator to detect the actual voltage at the battery so that the regulator can tell the alternator to increase its output to compensate for the drop across the charging wire from the alternator to the battery. In some cases, where your negative return is undersized, you may need to run the regulator negative back to the battery to get the equivalent of a negative sense lead. See further below for details.

If you implement solution #2 (my recommendation), it's okay to use your #4 red wire from the alternator to the batteries, as the regulator will adjust the alternator output to produce the proper charge voltage at the battery. However; you still need to address the negative return side. The preferable approach is to make sure the negative cable is heavy enough to introduce less than 0.1v drop at your max sustained charging current (likely 80-90 amps or less). Since you already need to run heavy (at least 1/0) cable from the engine to the batteries to handle the starter current, it's trivial to run a 1/0 cable from the alternator to the lug/busbar at the engine end of the negative battery cable.
If for any reason, you don't have a low-enough resistance negative path to maintain its drop to less than 0.1v, you can run the regulator's negative lead directly to the battery negative (instead of to the alternator). With a 1/0 negative return and carefully implemented connections, however, you should not need to do so.

If you are willing to spend the money and do the proper installation/configuration, I strongly recommend an external regulator that supports external sense, such as the Balmar MC-614. It could easily end up paying for itself in longer battery life. If you go that route, you should install the optional alternator and battery temperature sensors and triple-check that you enter the right configuration parameters for you battery type, etc.

* For this case we only care about the alternator current that will be sustained over many minutes. That's because it's about the efficiency of battery charging, not wire heating/safety. A 105A alternator is unlikely to output over 80-90amps for more than a few minutes due to both rising battery voltage and alternator heating.

Notes:
1. The negative path from the Alternator to the Battery negative terminal is at least as important as the red-wire positive path, yet the negative is often overlooked, sometimes relying on the case of the alternator being in electrical contact with the engine block.  It is important that there be a good heavy-gauge wire run from the alternator's negative output (there should be a bolt on its case) back to the battery (via a busbar or other heavy-duty cable-to-cable connection post is fine).
2. For reference, at 80amps a #4 wire will drop ~0.2v for each 10' of length.