Why does Hamlet delay killing Claudius when he was praying?I think it was because of his morals, his being a coward, and to his confusion about the...

Hamlet's decision to not kill Claudius isn't due to any of
the three reasons you
mention.

Morals aren't the
cause for the decision, because by that time Hamlet is certain that Claudius is guilty
of his father's murder (the play within the play takes care of that), so Claudius
deserves to die.

Hamlet isn't a
coward.  He is an excellent swordsman, as seen during his duel with
Laertes, who is reputed to be a great swordsman but is easily out-dueled by Hamlet.  And
Hamlet doesn't hesitate to act during Act 5 after Laertes wounds him unfairly, or when
he becomes aware that Claudius poisoned the cup.

And, since
the prayer scene is after the play within the play, Hamlet is certain that Claudius is
guilty, and the identity of the Ghost is no longer in
question.  As Hamlet tells Horatio:

readability="7">

...I'll take the ghost's word for a
thousand

pound.... (Act
3.2.266-267)

Strictly
speaking, Hamlet's Catholic beliefs suggest that Claudius's soul will be purged after
confessing, and Hamlet assumes he is confessing.  He's not, but Hamlet doesn't know
that.  Hamlet assumes he is.  Hamlet doesn't hesitate to strike out at the figure behind
the arras only a few minutes later when in his mother's chambers.  When he discovers
that the person he has killed is Polonius, he says "I took thee for thy better" (Act
3.4.33).  He thinks it's Claudius spying on him, and he doesn't hesitate to strike. 
What changed?  Claudius is no longer praying, and he is, instead,
spying. 

This, by the way, is seen by many as the climax of
the play.  When Hamlet decides not to kill Claudius because he doesn't want to send
Claudius to heaven, he is playing God.  Salvation is God's business, not Hamlet's.  If
Hamlet kills Claudius in Act 3.4 while Caudius is praying everyone from Polonius to
Gertrude lives; only the guilty party, Claudius, dies.  But because he delays here the
bloodbath occurs. 

Finally, though Hamlet's words
demonstrate why he doesn't kill Claudius while the king is at
prayer--

Now
might I do it pat, now 'a is a-praying,

And now I'll
do't--an so'a goes to heaven,

And so am I revenged.  That
would be scanned.

A villain kills my father, and for
that,

I, his sole son, do this same villain
send

To heaven.  (Act
3.4.73-78)

--there may be
more to it.  Some commentators see Hamlet as having a need to make what the king has
done public; to make sure everyone is aware of what went on and why Claudius must die. 
In this case, Hamlet doesn't really want to kill Claudius in private.  He wants the
truth to be known.

Finally, a third possibility exists: 
Hamlet is better at spontaneous action than he is at action preceded by thought.  In
other words, he is better at taking action when he doesn't have time to think about it
first.  If this is true, then Hamlet simply has too much time to think when he catches
Claudius at prayer.