I've been working through the same mess.
It just really depends on what you are keeping and what you are ditching if you want to try for top down or go bottom up.
If you can afford the down-time, for the most part it is easiest to just ditch everything and re-wire from scratch ground-up, especially if you are NA1 or are going with a different ECU and cluster. Just grab a generic harness, switch panel, supplies, etc... and DIY. Engine, lights, signals, etc... isn't too bad and it will be lighter.
For my application I wanted to retain Honda ECU, ABS, PS, TBW, letc... I also came to realize all the things you don't think about like wipers, lamps, signals, lateral sensor, etc.... although... trust me when you go top down... it can get really complicated to work on. Many of the stock wires are spliced half way into the loom and serve multiple functions. The wiring is also more involved on the NA2's. You will literally be backing out pin by pin on the connectors.
Their are pluses and minuses to both approches in terms of weight, servicability, reliability, etc... just really depends on what your goals are- minimum class weight, etc...
