Kant was a rational theologian. He did not pretend to be a biblical or revealed theologian.

Kant's description of most ethical duties reads more like a description of moral virtues and vices. Once we see this, we see that Kantian ethics is indeed a kind of virtue ethics, and that it does not "divide the heart from the head" (to anticipate one of your later questions) but instead recognizes the deep truth that reason and emotion are not opposites.

Kant does not think there is anything wrong with being beneficent from sympathy. He thinks we have a duty to cultivate sympathetic feelings by participating in the situations of others and acquiring an understanding of them. He thinks we also have a duty to make ourselves into the kind of person for whom the recognition that something is our duty would be a sufficient incentive to do it (if no other incentives were available to us). That's what he means by "the duty to act from the motive of duty".

We cannot predict the effects of our actions, especially our collective actions over generations or centuries, to use instrumental reasoning toward these big final ends to tell us what we ought to do.

Some of Kant's particular moral opinions, either because he shared the prejudices of his time, or because of his own personal crotchets, can strike sensible people as ridiculous or offensive. But in my view, his own theory provides us with the resources (the best resources available, I believe) to correct his own personal errors or cultural prejudices.

I think it is clear that what we ought to do has to be independent of our decisions about what to do, and independent of any procedures we might use in making such decisions.

Not only in order to act morally, but even to formulate theoretical questions, devise experiments, choose which ones to perform and what conclusions to draw from then - we must presuppose that we are free. That's the sense in which it is true that for Kant "we must assume we are free."