A very helpful thing to do is label both ends of each connector on your existing harnesses as you unplug them. Then lay those harnesses next to the new ones and label those connectors using your code. The labels can be the device name or a number/letter/animal code. Anything that helps you quickly identify and match up each end of the connectors.
Pictures of the out of reach areas or odd routing will help by creating a check list. I lost track of one of the connectors in the engine bay and couldn't find it for a long time until I called Blaine, described the connector and what area it belonged to. It ended up being for the AC compressor which was out of sight and difficult to reach.