I don't think it matters how the output shafts get punched into the pumpkin. In fact, I know it doesn't as I randomly shoved them back in when I did my gear swap. However, even though it's likely of minimal consequence to not match holes when mating the output shaft and 1/2 shaft, I also believe that Honda put that notation in there for a reason.
It would not be unreasonable to foresee that with a certain output shaft mated to a certain 1/2 shaft, that balance can be unique and critical. It is quite possible that in the OP's case, this could indeed have such a consequence. We use CVs because the angle of power transfer can alter and change at all times. CVs can wear in a particular way (wear patterns), developing grooves and nicks at specific places. If you rotate the orientation of 1/2 shaft to output shaft, new pressure points may be developed in the CV and we all know that a bad CV can be responsible for weird sorts of vibrations.
I did my gears relatively early my car's life, however, if someone were to do it later when the car's CVs have developed deeper wear patterns, I can see where altering this can produce adverse effects.

 

Clarifications:

The diff comes from Stratocaster / Ricks complete with flanges, so it doesn't matter where I marked my old diff for halfshafts or propshaft (and I did mark them). It doesn't seem to change when I turn / on gas / off gas / clutch in / clutch out-- so I'm hoping rotating the propshaft will cure and / or change the speed at which the vibration occurs. It feels exactly like my Jeep cherokee did with a bad u-joint.

Will update as soon as I give it a shot. Thanks for all the posts so far!

 

Try it anyway, but it may also be coincidence that one of your tires may have gone out of balance. Check for lost wheel weights and tire pressure and lugnut torque.

 

Will do... I know out of balance tires can vibrate, but this is really hard to localize to one side and I've never felt tires that vibrate THIS bad.

 

Do you feel the vibration on the bottom of your seat? If so, I would also check the pinion angle. Not sure if it plays on the S, when I lowered my Lightning it was very noticable.

 

Feel it in the seat for sure.

AFAIK there's no adjustment in pinion angle, but I know what you're talking about- had to shim my Jeep rearend when I lifted it.

 

I also have this same exact vibration and rumble noise with the new 4.57's. The gears and diff came from Ricks, and the whole assembly was swapped out by a local Honda shop. This particular shop has an S2000 guy too, if it makes a difference. Let us know how you tackle it and what works.

 

I was making reference to both the propeller shaft and the axles but I believe the prop shaft is the culprit. Let us know how it turns out.

 

^^i'd like to know also.

 

I rotated prop shaft about 90* and still feel the rumble / have the noise... Might be slightly lighter, but really hard to tell.