I know how easy it is to be intimidated by all the wires. I am at times when doing things on my boat. Take it one piece at a time. FWIW, adding on to previous advice:
1. Invest in a good "fox and hound" tone generator and probe kit. This makes tracing and identifying wires much easier.
2. Once identified and labeled, do NOT remove the ones slated for replacement until you are ready as they are excellent snakes.
3. Per previous poster, draw out a schematic (color coded) before you start.
4. Invest in a professional grade crimping tool (I have a Klein), strippers, heat gun, dielectric grease and a variety pack of terminal fittings. I prefer to pay extra for the ones set up with heat shrink, but you can go the regular route and purchase heat shrink tube separately.
5. Watch lots of videos on YT on how to do boat wiring. very helpful IMHO.
6. I have a copy of "The 12 Volt Bible". Very good reference book.
7. Do not be afraid to add extra passage holes to the liner in places where no one will see them.
Hope this helps.