I re-wired some stuff on my 460 recently but I kept the engine terminal block. (I don't pull my engine often enough to warrant the benefits of a clip harness connection, I also spray silicon and keep anti-corrosion electrical gel on the terminal block).
I did end up wiring a fuse box under my dash to control some extra stuff. I added to my boat such as toggle switch to control hydraulic trim, some usb ports, new light switches, and new gauges. I also fused my bilge pump.
For anything with a higher amp draw I would recommend reset circuit breakers.I prefer the manual reset ones vs automatic because then you have to physically reset the circuit and alerted of an issue vs automatics which will reset themselves after a delay.
Also maybe consider a battery selector switch. That way you can easily do any wire changes/diagnostics and quickly cut the circuit without have to disconnect the battery connections. Plus you can run two batteries if needed. Also if you are running constant circuits straight from the battery or that aren't switched, it gives you piece of mind your battery won't be drained when you to start the boat the next time. Some things have very low amp draw like USB ports/etc that could slowly drain the battery.
Power distribution blocks are also nice to have to minimize amount of wires connected to the battery and that way they can source power straight from the battery for more reliability (for me this includes bilge pumps and hydraulic trim pump). I put my distribution block in a water proof box along with the manual circuit reset switches.
In terms of constant power/grounds etc that is up to you. For my fuse block under the dash I grounded it off the metal bracket that supports my gauges which was already an existing ground vs running a long ground back to the battery or engine ground.
My key switch controls most of my circuits power. That way I can decide if I want some circuits on constant or key switched controlled. I guess this does put more load on the key switch control as a central point of failure but my boat isn't exactly pulling a ton of amps. You could complicate the circuit more with solenoids and reduce the load on the key switch eg, key switch only sends signal, solenoids handle the actual load (ignition, starter, etc) but that also introduces more points of failure. Just make sure you have a quality key switch.
In terms of sourcing wire, I used ebay was it cheapest for me to get the color/awg/marine rated/length I needed. I used heat shrink crimp connections.
I already had some toggle switch holes in my dash from original switches (didn't want to patch my dash), otherwise I would have put everything on Contoura III switch style. I use this toggle switches to control bilge pump operations (off, automatic/float, manual) and blower fan (enclosed engine).
Fuse Block:https://www.amazon.com/gp/product/B07CLS96RD/ref=ppx_yo_dt_b_search_asin_title?ie=UTF8&psc=1
Reset circuits:
https://www.amazon.com/gp/product/B08BKG1WQT/ref=ppx_yo_dt_b_search_asin_title?ie=UTF8&psc=1Battery selector switch:
https://www.amazon.com/gp/product/B00144B6AE/ref=ppx_yo_dt_b_search_asin_title?ie=UTF8&psc=1Power distribution block:
https://www.amazon.com/gp/product/B07THLYYH3/ref=ppx_yo_dt_b_search_asin_title?ie=UTF8&psc=1Example of heat shrink terminals:
https://www.amazon.com/gp/product/B07GB2JWVT/ref=ppx_yo_dt_b_search_asin_title?ie=UTF8&psc=1Toggle switch:
https://www.amazon.com/gp/product/B000N9MD5S/ref=ppx_yo_dt_b_search_asin_title?ie=UTF8&psc=1Contoura III Switches:
https://www.amazon.com/gp/product/B000Y87W54/ref=ppx_yo_dt_b_search_asin_title?ie=UTF8&psc=1Contoura USB:
https://www.amazon.com/gp/product/B01AHYC88A/ref=ppx_yo_dt_b_search_asin_title?ie=UTF8&psc=1Contoura mounting bracket:
https://www.amazon.com/gp/product/B000MMFK3I/ref=ppx_yo_dt_b_search_asin_title?ie=UTF8&psc=1None of these links are affiliated I promise lol.