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Randii, when I get to the slave cylinder mounting bracket I have a good idea about using a piece of pipe to mount the cylinder halfway into the bellhousing while still being able to remove it from the outside. This might prevent having to use a long rod.

Sounds interesting... you definitely want to be able to trouble-shoot and adjust from the outside.
FWIW, I don't see a downside to a long rod, as long as it is stiff enough. I've used threaded rod and coupling nuts to enhance adjustability, which adds value.

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My new problem is input shaft/clutch spline engagement... the splines end about 1cm before the flywheel surface and the clutch is only about halfway engaged as it is now. I'm assuming you would need the clutch disc to be 100% engaged on the input shaft splines at all times?

I'm not sure if I see what you're saying or showing. The friction disk splines need to be fully (or very close to it) engaged on the input shaft spline. Beyond that, as long as you have:
1.) full engagement of the clutch and flywheel plus a bit of airspace between the throwout bearing and the pressure plate fingers, and
2.) full disengagement of the clutch from the flywheel, plus a bit of airspace between them

Any of your suggestions should help fine-tune this. I think shaving the bell is path of least resistance, as mucking with the crank or flywheel needs done delicately to maintain balance. There are also vendors out there that could also build a friction disk with custom offset (sometimes just a 180* flip), but finding a machine shop to shave your bell (careful with that vowel!) will be easier, assuming you have thick enough flanges and faces on the bell... how thick are they?

If you use any of the above methods to change the alignment of the flywheel relative to the front face of the bell, you'll need to compensate with a simple spacer for the starter. That should be easy, though, since it won't need to be balanced, and can be flat stock with basic grinder work (unless you have access to plasma, waterjet, laser, etc.).

Randii