Sorry about how long it's been since the last update!
With the OEM-spec head gasket on cleaned mating surfaces, I torqued up the cylinder head to the block with new OEM bolts as per service manual.
Installed some plastic shrouds, a main engine mount hard point, cam pulley, distributor, and then installed a Gates timing belt kit (timing belt, tensioner, water pump) with the crank position sensor.
In order to install the timing kit, I needed the main pulley / harmonic balancer and woodruff key for same. Afterwords, I needed to remove the main pulley to install the timing belt outer cover, and naturally the key dropped to the floor. I heard it hit the floor, and I even thought I saw where it bounced. Much searching later, it is pronounced lost. Later, I buy the replacement at Kuni Honda's parts desk.
After that, more engine externals went on, starting with the main pulley, a new key, and new bolt. The bolt comes with replacement/revision pages for how to install it (vs field service manual), which involve overtorquing, detorqing, retorquing to x ft-lb, tightening the bolt 60 degrees, a heat cycle on the engine, and then turning another 30 degrees. I stopped at 60 degrees.
Using feeler gauges, a screwdriver, and a 8mm wrench, I reset the valve clearances to spec with each cylinder at TDC. After that, I dumped some 5w-30 over the valvetrain before sealing the valve cover down with a new gasket and service-manual specified silicon sealant on strategic corners. I also flooded the oil filter port with oil in an effort to ensure the oil pump would prime quickly.
New o-rings on the water pipe out of the water pump and to the thermostat housing. New o-ring on the crankcase breather box. New PCV valve. Reinstalled knock sensor, oil pressure switch, drain plug, VTEC solenoid assembly.
At this point, I rolled the engine on its stand out onto the deck. I threw two short 2x6 boards down over the four steps from the deck the the driveway, and very carefully backed the engine stand (with engine) down this impromptu ramp. At the bottom safely, I dragged it to the front of the 2000 Civic EX sedan.
I pulled the engine hoist out of the shed, transferred the engine from the engine stand the the hoist. While there, I installed the drive plate (used instead of a a proper flywheel on the auto tranny versions). Next, using the engine hoist in tandem with a transmission floor jack, re-joined the tranny to the block.
I took this opportunity to reinstall the intake manifold with throttle body and fuel rail / injectors. I also bolted the torque converter and drive plate together. With much effort on the soft dirt driveway, I maneuvered the engine hoist into position and carefully lowered the engine into place. In reality, it was an endless succession of minute position adjustments to get the rear mount bolt in place, and then from there it was pretty quick.
While this really felt like progress, there was a ton left to do. Fortunately, from engine-in onward, it's all-too-familiar stuff.