I have decided to replace the engine in my 89 Si (300k miles, it needs a rest).
I am going with a DOHC ZC engine. I plan to put new seals, gaskets, timing belt, water pump, clutch and pressure plate before I install the new engine. Where do I find these parts? Since this is a JDM engine the guy at NAPA won't have a clue.
Any recommendations for other parts that should be replaced before installing the engine?

http://www.d-series.org/forums/dohc-zc/91053-dohc-zc-specs-mods-parts-list.html

Just replace all the parts you've listed, as well as spark plugs & wires and the thermostat. If you want to go even longer without having to worry about parts failing because of age, a new distributor, alternator, and possibly a new oil pump would be good.