I did the same thing. It was fun and I learned a lot in the process. I too did not want to buy the generic harness. Easier to make it for your boat, will turn out nicer IMO.
What I did was first decide where I wanted my terminal block to be mounted. I wanted the wiring to be stealth so i mounted it in a place where it would be easy to hide the wires yet allow access to the terminal block. I mounted in the front of the engine on my direct drive alternator mount, and ran the wires through a gromet and under my rail then to the back of the motor, up through another grommett in the rail and to all the senders/starter/solenoid.
Having the terminal block on the motor allows easy disconnectionfrom the motor for removal. So yes in essence there is a separate harness for the motor.
Instead of starting at the battery, I started at the dash. I made up a power wire "in series" for the gauges. 12V power on a single linked wire instead of 1 wire for each gauge. Turned out very clean this way. Did the same with the ground wire. Ran the wires to the terminal block and then worked on wiring the senders.
Rambling...anyhow, take your time and do it right. Use a nice crimper and heat shrink every connection and it will look really nice. Think about how you want it to look and where you want the wires run before doing it.