Wiring kit help!

I put an EZ harness in my 40 Ford. It was a total piece of cake. I understand your frustration though. You need to break the project down and address the areas that are troubling you which include your having to deal with a job that seems to have been hacked by the P.O., your lack of familiarity with wiring automobiles and a wiring harness that is pre configured to a degree for a late model GM column which is where most wiring kits attempt to save you time and labor by pre-terminating some of the wiring with the GM standard connectors to be used at the column, the headlight switch and the dimmer switch.

For now, ignore the connectors and try to understand that the basics are the same no matter what brand of kit or column you are dealing with.
All power originates at the battery
All grounds need to be tied back to the battery
Think of the fuse panel as a "distribution point" for the battery power
There will be some confusion due to the fact that power from the fuse panel gets routed to things like the column and then returns back to the fuse panel. This is especially true of the turn signal and stop light wiring.

All in all, try to envision each electrical function as a circuit, that is to say, there is an origin of the power, routing to the powered device through some sort of a control or switch and finally a connection to ground to complete the circuit.