"The was no dignity that night:
the shepherds slapped their sheepish knees
and tasted too much of the grape..."
No dignity and no faith - that appears to be what is happening in the poem, despite the fact that all of its characters are the major characters of Christianity. By saying that the shepherds had too much to drink, the poem is saying they are drunk, and have lost their dignity. They are no longer able to precisely do the job of religion at hand, and this will cause a problem for all of the believers in Christ.
"The apple I see and the apple
I think I see and the apple
I say I see
are at least three
different apples..."
The narrator begins in a rather pessimistic tone, by describing that he has been lying his whole life. Perhaps not his whole life, but the narrator has admitted the deed of lying through the metaphor of apples, a simple fruit that comes in all sizes, colors, and shapes. The narrator actually has a standard apples - one not that perfect, a little discolored, and perhaps with a bite out of it. He sees, however, a perfectly fine apple, one fit for eating. He says he has the greatest apple of all, and is prepared to share it with everyone. Obviously, he only has one "apple", but wants to say and believe for himself that he has more.
"Of course we're as innocent and guilty as either of
those doomed..."
In the poem "M?", or M3 for the element described within, it is said that a completely unrecognizable element was slipped into the water supply of the Earth long ago. Humans have not been able to find it, and that fact scares those that believe it exist. What if they were drinking something that they didn't know was there, and it was potentially harmful? People "doomed" by the element are said to be just as guilty as those not, because the people failing to accept the fact that M3 may exist are ignorant, which is one of the worst crimes of all.