The risk of relying on the OEM wiring diagrams for this kind of stuff is that previous owners may very well have "improved" the boat with their own modifications. On mine for example, the solenoid was manually activated by a breaker instead of by the ignition power...
1. Identify your goals and use cases.
a) what will be your charge sources at the dock?
b) what will be your charge sources while under way (engine) ?
c) what will be your charge sources at anchor?
d) How do you use the boat? live aboard ? weekends? overnight at anchor or at the dock? do you run a toaster and espresso machine in the morning or use the propane stove for cooking? Are you pulling the propane gear out and going all electric? Will you maybe go all electric in the future?
e) where do you cruise? how much sunlight do you get? does the boat have solar?
f) what alternator (s) do you have? do they need to be upgraded to match the new lithium house bank? There's no point having 1000 Ah of lithium if you only charge them at 30A with a dc-dc charger while under way.
g) do you have a generator? are you keeping it?
h) do you need/want to run AC on lithium? many of the new Air Cons work well on batteries/inverter, if you have enough solar and sun to keep up
2. House batt charging
to get the full benefit of Lithium, you really want to charge your house battery from the alternator. This means installing an alternator regulator that has a temp sensor and regulating the charge output based on alternator temp. Alternators are designed to run up to 100 deg C. Limiting this to 80 deg C will extend the life of your equipment.
some boats have 2 alternators. a small one for the start batt, a large frame one for the house batt.
This means you probably want a means to charge the start battery .... this is usually accomplished with a DC-DC charger. You can setup the DC-DC charger to only activate when the ignition is ON (recommended). This way, on shore power, you can have seperate 120V charge sources (inverter/charger for house bank, and a 7A 120V charger for the start batt).
3. Engine starting.
Do you want to start the engine only on the start battery or be able to use an emergency crossover from the house batt? Many of the modern Lifepo4 BMS have a high enough current limit to start most small diesels. You can do this with a 1/2/off switch (for engine starter) or with an ON/OFF switch for the start battery and then an emergency parallel switch to link the house batt to the load ide of the start batt on/off battery switch.
4. Boat audit
Before doing anything, I'd spend a day crawling through your boat and drawing out the DC/AC electrical system. This includes pos, neg, neutral, bonds, etc.... Everything from the AC input shore power to the AC circuit breakers. Then everything from the batteries to the DC panel breakers / alternator / starter. Note wire gauges for the DC size, fuse types and sizes.
5. Design
Once you have a detailed wiring schema and know the fuse sizes, wire, sizes, etc...
a) select your batteries. where will they fit? what will be the wiring run lengths? If you parallel multiple batteries, ideally the pos and neg wires from the batt to the bus bars should be identical length. From there, you will have class-t fuses and then cabling going elsewhere in the boat.
b) Hot (always on) dc bus. This is for your charge loads that are not disabled with your normal on/off house switch. Ie: shore power charge,MPPT chargers,Inverter/Charger, etc...
Note: you'll need a service disconnect (on/off) at the battery and at the alternator. I also install them for the cable from the hot dc bus to the alternator so I can work on the engine safely without shutting off dc power).
c) alternator / regulator. You need a means to regulate the output to avoid overloading the alternator. Wakespeed, Electromaax make good regulators. If you have never programmed these, I'd suggest hiring a professional that is familiar with your regulator and batteries. Mistakes here can be costly
d) load dump. In case there is a design error, your BMS may disconnect the batteries. Not an issue on shore power, but running on alternator this can be very expensive. Balmar and others sell a load dump to catch the voltage spikes should this happen.
e) wire chases. do they still have room? is there pull strings in them or do you need to spend 2-3 days pulling strings in each chase?
f) Draw it out. If you've never wired a boat from scratch, it might be worthwhile to hire a marine electrician to design this for you. Some marine electricans will do this remotely. Pacific Yacht systems does a lot of remote design. They will draw out a detailed system diagram and help you select components to achieve your goals.
Pacific Yacht Systems: Marine Electronics And Electrical Systems, Marine Boats Vancouver, Sailboats Vancouver, Boats Electronics (they also have lots of resources such as youtube videos, how-to, diagrams, etc...)
g) Windlass. Once you go to lithium, you can switch it from the start batt to the house batt. Some boats have a relay that only power the windlass when the alternator is running. I usually disable this as I want to be able to use the windlass in an emergency at anchor without having to start the engine. Bow thruster .... you have options. Some use a DC-DC charger, some wire it to the alternator, etc....
Once everything is figured out, it's about a week's work for an experienced marine electrician. If you haven't crimped and heat shrunk several thousand connectors, plan for 3 weeks. You'll need a lug crimper (not a hammer!), good terminal crimp, good quality terminals and heat shrink, support cables every 18 inches.... It may be worthwhile to buy access to ABYC standards while you do this project.
In terms of costs, if you do it yourself: Add up the cost of the new batteries, inverter/charger, MPPT chargers, solar panels, etc.... Then add 50pct to that total. That will roughly cover fuses, wiring, switches, terminals, and other supplies.
On our H38, we were at about CAD $10 000, diy (600W solar, inverter/charger, CerboGX, new switches, alternator regulator,630Ah lifepo4, wiring, fuses, bus bars, terminals, tools, etc...). I figure I spent about 70-100 hrs on the project at the boat, not counting research and design time at home or the time I spent auditing the boat and pulling strings in all the cable chases. A dock neighbor hired a marine electrician for the same on his Beneteau 391, took them just under 2 weeks.
For now, you might enjoy going through the PY Systems videos and tutorials on their website? Victron also has lots of sample installation diagrams.
Given the cost of the equipment, this is not a good project for someone new to marine electrical. Making a programming mistake can damage thousands in hardware or make the power unreliable away from the dock. If you have difficulty following the wiring diagrams in the OEM manual, it might be a good opportunity to learn by finding a marine electrician that will allow you to assist them with the project. You'll get to learn how to do and will understand your boat and systems very well by the end.
That's a big jump from a 29 to a 49! Have fun. Don't cheap out on components..... look for high quality packs, ideally those that communicate with Victron (SOK, Epoch, Victron, etc...). Program all your charge sources conservatively at first (ie: 13.7-13.8V), lower alternator output and inverter/charger output and monitor how the system does.