half shafts orientation

As long as the u-joint crosses are oriented such that the ends are parallel to each other, then yes, the half-shafts can be separated at the slip-joints and even partially replaced without affecting balence. At least at any speed up to 150 mph (all that I can personally verify to). Where we get into trouble is when the halves are stuck back together a few splines off so the crosses aren't parallel. Then you'll get pulsations while driving.

As long as the u-joint crosses are oriented such that the ends are parallel to each other, then yes, the half-shafts can be separated at the slip-joints and even partially replaced without affecting balence. At least at any speed up to 150 mph (all that I can personally verify to). Where we get into trouble is when the halves are stuck back together a few splines off so the crosses aren't parallel. Then you'll get pulsations while driving.
As for the balence of clutch & flywheel, the flywheels on all Fords are balenced identically, while clutch covers and discs are zero-balenced (that is, neutral) so they can be bolted on in any orientation without affecting balence. Flywheels use an asymmetric bolt pattern so yiore forced to attach it the proper way. Non-stock hot-rod parts may be a different story; check with the mfgr for their requirements.

I can't speak for the rest of you, but my half shafts have two arrows that line up, one on each side similar to timing marks. Just match them up and you should be there.

Thank you.