When the gearbox is mated to the engine, how much of the input shaft rests inside the bearing? I'm asking since my built engine came with a Kennedy clutch and flywheel and from my measurments it seems there will be very little bearing support to the input shaft?

On 914-4's the pilot bearing is in the flywheel, while on Busses, it's it the crankshaft, not sure where your's is.

It's in the flywheel, 3.2 mm from the boltface according to the picture in the Haynes manual.

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So here's the engine side measurments. The only dimensions thats important are
the mating Surface to flywheel edge (42,5 mm) and flywheel edge to pilot bearing edge (40,9 mm)

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Here's the gearbox side, the important dimensions here are the input shaft nose to the mating Surface distance (10 mm) and the 22 mm distance from the shaft nose to the start of the splines. My guess is that the pilot bearing should rest on the flat
part of the 22 mm dimension.

Click to view attachment

This is what it looks line when I align the Engine and gearbox mating Surfaces.
The flat part of the input shaft only rests with 2.8 mm inside the bearing which means its barely touching the needle rollers.....

It this enough? Dr Evil, confused patient seeking consultation....