Hmmm... mine doesn't have any plastic tubes. Just the diagonal-cut
copper tube that's supposed to magically slip into the rubber grommet
on top of the water pump. It's not long enough to allow for aligning
before the lower unit is completely attached. I did use a dental mirror
and flashlight to look at the alignment yesterday afternoon, and I
figured out that if the leg of the motor is absolutely vertical the
tube hangs naturally near where it needs to be. I may yet take it apart
again and see if I can find something to make a tube guide for it, but
considering the proximity to the driveshaft there won't be any room for
error.

Airthug wrote:
My 2 plastic tubes are slightly different lengths.
I was able to reach in with my finger & guide each one into place, onto
the copper tubes, then turned the flywheel to send em home.
I stuck them to the pump with a little RTV.