With regard to the first problem, if Logan is going to keep his silence, then the writers need to find external ways to express this conflict. As it is, Father Logan just mopes around doing nothing.
What little action there is comes to a halt during a long flashback in the courtroom scene (48-58 min.), so we can learn of Logan's romantic affair before he became a priest, which supposedly gives him a motive for the murder. Long flashbacks are very tricky. They can work, as in Casablanca, but in order to work there must be considerable momentum built into the present-tense story to keep the audience hanging. This is not the case here.
The inactive, passive Father Logan is the central problem here. Even keeping his silence about the confession, he needs action, dramatic ways to externalize and show his inner conflict. This is the kind of story that is best told in a novel, where the inner life can be revealed, rather than on the screen, where nothing is happening most of the time.