The mechanics of salvation
I had already drifted away from orthodox Christianity when I began to think about the following problem, but right now I'd say it's one of the biggest stumbling blocks to ever returning: How, exactly, did Jesus manage to die for our sins? In other words, what made his death necessary and sufficient to forgive us? Why couldn't God simply forgive us before Jesus' execution, and why did he have to forgive us afterward?
Growing up in the church (ELCA, to be specific), the most common framing was that Jesus took our punishment on himself. God demands that we live up to an exceedingly high standard of moral perfection, but since human nature was damaged by the Fall, we inevitably sin and thus wind up deserving eternity in hell. But by dying on the cross, Jesus took our punishment for us and so we're free to go to heaven. The imagery here is typically of a person facing God on Judgment Day and having God pronounce our sentence, at which point Jesus pops up and says "no worries Chief, I took care of it."
But this idea of Jesus taking on other people's punishments is nonsensical from the perspective of justice. Imagine trying to do a similar thing in a human courtroom. Someone has been convicted of a crime, and the judge sentences them to several years in jail. Just then, a member of the audience jumps up and says "Your honor, I will serve this man's sentence for him." By what logic would the judge agree to this deal? It's not enough that if there has been a crime, *someone* gets punished. Every theory of punishment -- retributivist or consequentialist (deterrence) -- requires that the punishment be inflicted on the particular individual who committed the crime. It accomplishes nothing to punish an innocent third party.
It is possible for a judge to be satisfied by punishing the wrong person in one scenario -- the scenario where the judge does not know the wrong person is being punished. But it seems rather odd to premise an entire religion on one part of the godhead playing an eternal trick on the other part. And it's hard to reconcile the idea of Jesus tricking God into accepting the punishment with God's omniscience, and with the Bible's claims that Jesus' life and death were a mission he was ordered by God to carry out.
On top of that, Jesus was not actually crucified for our sins. He was crucified for (allegedly) fomenting rebellion against the temporal and religious authorities in Judea. So perhaps in my example above, we should really have the audience member jump up and say "Your honor, the other day I was beaten up by a mugger. Please count my injuries as the punishment for this man's crimes." That makes even less sense than the original scenario.
Another common frame is that Jesus' death "paid our debt." In this frame, the punishment we deserve for our sins is not some sort of retribution or deterrent -- instead, our sin causes some sort of loss to God, which needs to be repaid. Unlike punishments, debts can clearly be paid off by a third party. A pure creditor doesn't really care where the money comes from as long as they get it back, on time and with appropriate interest. This model fits with the animal sacrifices made by Jews during the temple era -- and indeed, Jesus is often explicitly analogized to a sacrificial animal. Animal sacrifices work because the deity -- be it Yahweh, Zeus, or Baal -- actively enjoys the death and burning of an animal, and that enjoyment offsets their anger at the sacrificer's sin. (Animal sacrifice also often contains a claim that the sacrificer's economic loss is important because it demonstrates the depth of their concern/contrition, but that raises two problems in the Jesus case: first, it brings back the third-party problem noted with respect to taking on a punishment, and second, Jesus' death is not actually a loss, economic or otherwise, for those who get saved by it, since he came back to life three days later.)
A key element of the debt model is that debt only works if the creditor values the thing that's owed to them. If somehow someone ended up owing me a giant pile of manure, I would not ask them to pay it back, since I don't want a giant pile of manure. So God has to intrinsically enjoy the suffering that he's owed -- God likes watching people burn in hell, and he likes watching his son get crucified (likes it, in fact, exactly as much as he likes watching all the people who ever lived burn in hell for eternity). That's a pretty gruesome God we're being asked to worship. Nevertheless, people have worshipped some pretty gruesome deities in various times and places, and "gruesome" is arguably more consistent than "loving" with much of God's conduct in the Bible.
More important, though, is the question of why God doesn't simply declare our debts cancelled without indulging the sadism/masochism of killing his son. After all, no matter what you owe me, I always have the prerogative of declaring it void (and indeed, God specifically ordered the Israelites to cancel all debts every so many years). While there's an argument to be made that strict adherence to justice forbids granting mercy in cases of punishment, there's no similar argument that justice demands not forgiving debts if the creditor is so inclined.
A final bit of imagery I often heard in church was that Jesus' blood washed away our sins. It's quite opaque to me what, if anything, this metaphor tells us about how he accomplished that.
So in addition to the doubts I have about whether Jesus' life, death, and resurrection actually occurred in anything like the form described in the Bible (on which I may post later), I'm stumped as to the mechanics of his death leading to forgiveness. "Jesus died for your sins" seems like a non sequitur.