The cast in place water tube never does seem to line up perfectly with the opening for the grommet. Not to worry as it will flow enough water and the offset also acts as a stop for the copper tube. The copper tube will bottom out against the casting when its pushed into the grommet.
A silicon based grease such as Sil-Glyde brake lubricant works wonders helping to seat the upper grommet properly. Removing any corrosion from the bore and running a proper size drill bit thru both holes for the grommets tabs will also help. If everything is clean and lubed, the grommet should install quite easily if you have an installation tool. The retaining tabs have to be fully seated in their holes or it will be next to impossible to slide the copper tube in.
Here’s an installation tool I made out of some 5/8″ round Acetal plastic. The grommet fits on the end and it is relieved to allow the tabs to fold in while its being pushed into its bore. A little bit of silicon grease, a little push and a wiggle to make sure the tabs are properly seated and you are done.
This photo is of the lower crank seal on these motors. Like Frank said, they weren’t the best design and it should be replaced while the powerhead is off. Might as well do the upper seal to while you’re at it.
