I read in All Data site and have confirmed it online that one is supposed to make the zero marks on flywheel and clutch cover be approx. 120 degrees apart. There is only 3 places that the housing can be placed because of the alignment pin.  I was unable to discern any mark on the new clutch housing indicating a zero. Any ideas?

Sorry I meant to say alignment between clutch cover and flywheel 

If the cover can be installed in more than one way, then it doesn't matter. They generally recommend re-installing a cover in the same orientation to the flywheel if you need to remove it for some reason other than to replace the clutch. This is so that any wear of the components does not throw off the balance of the assembly. In this case you would just make a mark on each and reinstall with the marks lined up.

If installing an all new clutch and cover plate, then it doesn't matter because the parts are balanced individually, and ideally you would have the flywheel resurfaced which should work out any imbalance. Most machinists re-check and adjust balance after machining a flywheel.