The washer (red arrow) you left behind needs kept with the starter drive also verify the other washer for the bendix drive is their, I cant count the Pilot engines I have rebuilt that has had these washers missing, I even stock these washers it happens so often.
Check for how much metal dust is stuck to the magnet inside the trigger (blue arrow) also look inside the flywheel metal dust and DIRT accumulates their also, on the Honda Z50 engines the flywheel is your oil filter and is usually full of clutch dust, blow by sediment and dirt that has entered the Engine.
Fill the bearing up full with oil (green arrow) whilst the case is in storage this also protects the black rubber seal behind the bearing, carefully scrape all the gasket material off the case, use not chemical cleaners inside the case you can only damage the electronics or the bearing and seal, wipe out as much dirt as you can feel the need to wash it out then use 5w
Engine oil to flush it out, then put the entire case inside a 2 gallon zip lock and zip it up to keep it dry and clean they are a dust magnet.
If you remove the key from the crank shaft it gets stuck inside the flywheel to a magnet for safe keeping and until you install the flywheel again, find the case dowels remove and stick them to the flywheel also these are the second most missing parts from a Pilot Engine not sure how they get lost and how they never get reinstalled but they do.