Welcome to the forums!
If you fit an automatic bilge pump, it needs to be wired direct (with appropriate fusing) to the house battery, and it should be plumbed to a dedicated outlet, following the pump manufacturers instructions on a gooseneck, etc. However, check first to see how dry the boat is after a few months, you may not need a pump. The only thing in my bilge after 8 years is dust! And remember that a small auto pump won't cope in the event of a major leak.
It's likely that, in almost 20 years, previous owners will have fiddled with the wiring, so you just need to trace circuits.
I never leave my boat plugged in to shore power when I'm not there. If you plan to use shore power frequently, it would be worth adding a galvanic isolator.
I've not heard of a system which prioritises nav lights. Is the manual you're referring to a Bavaria manual? Or something put together by a previous owner?
OK to add LED lights to the existing circuit.
The location of the diesel heater isn't set in stone; you can put it where you like. However, give due thought to ducting runs and exhaust routing. If you can, arrange a smaller diameter duct feed into the heads.
You don't need an inverter to charge a laptop - a simple car adaptor works fine. If you do decide to fit an inverter, don't wire it into the boat's mains circuit, there are big safety issues. The cheapest, simplest and safest way is to hardwire the inverter to one or more dedicated outlet sockets. I have a 2000W inverter wired to an outlet in the heads locker (for using a hairdryer) and a second outlet in the galley (for the kettle and microwave).
I'd caution against using any type of wireless navigation instrument - hard-wired is infinitely simpler and more reliable. Whether you can export plotter data will depend on the plotter model.
An autopilot is a major advantage; ideally fitted below deck with a linear drive system.