My two cents in trying to answer your questions:
1. Should you replace the plug wires at the same time I replace the engine wiring harness? Absolutely. The plug wires see high voltage and are subject to heat and deterioration over their life. Be sure and also replace the plug connectors under the coils since they are usually the first part of the ignition wiring to malfunction (too much heat).
2. Should I cut wiring to fit, or can I buy the connectors with pre-cut wire? You can do it either way. Fully assembled wire sets can be purchased from Fastlane (about $100 +/-). Or you can purchase the resister boots and cut your own wires to length. Assembly is easy. You just cut the wire with a pair of diagonal cutters and "screw" the wire into the connectors which have a threaded post protruding from the connector. Use a little bit of silicone lubricant to wet the wire ends. This eases assembly and takes some of the twist strtess out of the wire as you screw it into the connector boots. Whatever method you choose.....be sure to replace both the wire and the connectors!
3. Should I replace the coils while I am at it? Not necessarily. Though the coils are subject to heat, they are a lot more stout then the wiring and connectors. They usually don't degrade in performance either since there are no wear and tear parts. They are also relatively expensive (about $300 for the set). They are also relatively easy to replace at any time, so you might want to save your money and not replace until they fail........which may be never!
Hope this helps.