One end of the pilot bearing (aka, spigot bearing) has it's part number engraved on it. That end is to face out of the crank as installed. Just inside the bearing on that end there is a little rubber seal, and there is no seal on the un-engraved end. The rubber seal must end up outer-most when installed.
The bore in the back of the crankshaft is surrounded by a large tapered recess, like a very over-sized countersink. The bearing is pushed in until it is flush with the flat rear face of the crankshaft, NOT to the bottom of the recess. That leaves the end of the bearing standing a little exposed from the bore.
Install the flywheel, then install the clutch, using an alignment tool to center the disk duriing the install.
When it comes time to mate the transaxle to the engine, slip a fresh Nylatron washer onto the small end journal of the input shaft (ie, the 'pilot' or 'spigot' journal). Now, when the transaxle is installed, the parts order you asked about will be pilot bearing, Nylatron washer, input shaft. Just like the close-up illustration Atwell posted.
The Nylatron washer is an easy slip fit on the input shaft's pilot journal, and there is no retainer. It just ends up trapped/ squeezed between the pilot bearing and the shoulder on the end of the input shaft.
While the transaxle is being installed, take care to maintain forward progress. That way, anything that might catch on the Nylatron washer will be pushing it back against the shaft's shoulder. If you ever run into a problem and have to back-up, there is a risk of the Nylatron washer being hooked, and pulled off the end of the shaft. 'IF" you ever have to back-up, then back-up far enough to visually inspect the washer and ensure that it's still in place. Be aware that it is all too easy to inadvertently pull the washer off inside the clutch housing where it's out of sight.
Before installing the transaxle, buy two long bolts. BOLTS have a short thread at the end, and then a long, smooth shank. MACHINE SCREWS have threads all the way to the head. So, buy two long bolts, cut off the heads, grind a generous taper/ chamfer around the cut-off end, then use a hacksaw or Dremel/ cutoff wheel to cut a screwdriver slot across the end.
Install the bolts in the cylinder block's rear flange, in the left and right side holes that also accept the ring dowels. I don't have a length dimension for you, but the bolts should be long enough to engage the bell housing holes about the same time the end of the input shaft engages the clutch housing. The bolts will serve as guide pins for the transaxle, helping to keep it aligned with the engine as you slide it into position. Just one less thing for you to worry about when there's a lot of stuff going on.
It's also important to keep the transaxle "on-axis", and not tilted up or down, left or right. To do that, keep an eye on the gap between the bell housing and engine block, all around. Keep the gaps top & bottom, and left & right equal as you move the transaxle forward. I like to cut scraps of wood. 2x4, then 2x2, and finally 1x2. Slip a wide spacer into the gap and proceed until the bell housing makes contact on all sides... square it up. Then swap in the next smaller spacer, and go a little further. As soon as the bell housing is close enough to engage one of the longest regular mounting bolts, even if it's not in it's correct hole (or buy a selection of different length bolts for pulling), use them to pull the transaxle forward instead of trying to push it by hand. By the time the bell housing has made contact with your thinnest spacer block, it should be very well aligned with the engine, and the input shaft spline should have engaged the clutch disc's spline.
If the shaft & clutch splines butt heads rather than slip together, just put the transaxle in gear, grasp both output shafts, and rotate them both back and forth in the same direction. That will cause the input shaft to rotate as you force it forward against the clutch spline. That should help the splines engage easily.
When the bell housing finally contacts the block, remove any temporary 'pulling' bolts you may have used to draw the transaxle forward, and start installing all the correct bolts in their proper holes. Finally, use a screwdriver to remove the two long guide pin bolts, and replace them with the proper assembly bolts.
PS... If you're uncertain, ask questions prior. Don't ask for confirmation after. After can be expensive in terms of both time and money. Try to keep the 'tuition costs' on your learning curve as low as possible.
Last edited by Esprit2; 06-18-2017 at 10:59 AM.