SAN FRANCISCO -- John Paul II did not spend all his time among us as an invariably untroubled guest, and he would probably think himself faithless to his duties if he had not now and then been a troubling one.

It would be one of the sin of pride's more extreme follies for any of us to claim to understand him completely, but we cannot travel even a little way along that road unless we appreciate the degree to which he came, refreshed us more perhaps than we did him, and then departed, still a little the stranger who had been in our midst. John Paul defined the spiritual distance between himself and America most directly when he spoke in Spanish to what has now become the largest part of San Antonio and said:

''We cannot make up the faith as we go along.''

That is not an American notion. The United States was born unique among nations for having from the outset thought of itself as invented by itself. Our ancestors were polite enough to God to invoke and acknowledge His help, but they conceived of their work as primarily man-made. How then can we not be puzzled when we are denied our license to make up a faith as we go along? Haven't we always? Is it not almost our birthright?

But the difference between this particular pope's spiritual tradition and our own is far less important and altogether easier to bridge than the tidal fact that he has been hard used by the world and that most of us have not.

His morning began Friday in a dialogue with two representatives of the Catholic laity. He was addressed with eloquent candor by Donna Hanson, chairwoman of the U.S. Bishops' National Advisory Council:

''Can we be as inclusive as Christ, who reached out to the woman at the well, who invited a tax collector to be an apostle, who brought the centurion's daughter back to life? Can we reach out and be more inclusive of women, our inactive clergy, homosexuals, the divorced and all people of color?''

The pope had read these words well before she spoke them: all these public dialogues are prepared and approved in advance. He listened to her with a solemn repose occasionally altered by one of those turnings of his head and entries into remote silences that suggest an inner voice reciting the poem that he wrote when he was a cardinal and that begins, ''I am bound to the world and besieged.''

But then, such moments of ruminating abstraction arrive just as often when he is being fervently accepted as when he is being delicately questioned; and there was no sign that Donna Hanson had said anything that abraded his comfortable and approving assurance that he and she were one in the spirit.

And then, with a smile the more charming for being so shy, she asked him to ''allow me to walk.'' ''Please let me walk with you so that I can understand what it means to be Peter's successor. Let me share the burdens you carry as you reflect on the pain of your people: persecution in your beloved Poland, starvation in Ethiopia, consumerism in the U.S.''

At the mention of ''persecution in Poland,'' he stirred from his immobility, lifted his hand and shrugged one shoulder. That tiny gesture seemed somehow a signal that here alone they could not be as one, because she was not a Pole who had lived under the Nazis and the Communists, and that Poland was one place she could not walk. It was a faint and transient hint of impatience.

That gesture might explain some of the coldness of his parting with the Jewish leadership after its Sept. 11 talk with him in Miami. Few of those present could remember experiences of direct suffering from the Nazis as intimate as his own. Of all the peoples of Europe, only the Jews were treated more savagely by Hitler than the Poles. The wound the Jews feel because Pius XII was not loud enough in their defense could be one he shares with them. Pius XII did not speak up with much noticeable thunder for the Polish church even though its congregants were sheep more devoted to their shepherd than any others in Europe. There must have been times when the young Karol Wojtyla, hiding in his underground seminary in Krakow, wondered whether he and his countrymen had been abandoned by the Vatican they revered as the seat of God. He could only have said to himself, ''Yea, though He slay me, yet will I cling to Him.'' Those words are by no means the least primary among the articles of faith of a messenger who confuses us, of all people, most especially when he preaches suffering as the only way to salvation.

Much and perhaps too much had been made of his differences with his American bishops. Most of the gentle remonstrances he not quite gently rejected had all to do with the cosmetic and none with the cosmological. The church, Archbishop John Quinn suggested, ought to find ''more effective ways of translating {its} teachings into more attractive language.'' Archbishop Rembert G. Weakland of Los Angeles reminded John Paul II that ''Catholics in the U.S.A. are jealous of their tradition of freedom . . . and an authoritarian style is counterproductive.'' Cardinal Joseph Bernardin of Chicago wished rather wistfully that ''when someone questions how a truth might be better articulated or lived today, he or she {would not be} accused of rejecting the truth itself.''

These are not the soft reproaches from which schisms gape. He prefers the uncomplicated sort of Catholicism that knows it is sinful and strives to become virtuous. So, we ought to assume, do his bishops. They no doubt find it curious -- and he must find it appalling -- how ready Catholic laymen are to answer the pollsters who solicit their opinions on matters of doctrine. The pope and the American bishops are more than resigned to a church of sinners, but they can be excused some want of tolerance with sinners who presume to redefine their own sin so as to expunge it from the calendar.

Three AIDS patients die every week in the 15 beds of the Coming Home Hospice, in what used to be a convent of teaching nuns at the Most Holy Redeemer Church in the Castro district of San Francisco. They die in the arms of the church, and the women of the parish held bingo parties to raise $60,000 toward their hospice.

Homosexuals are welcome as worshippers at Holy Redeemer. Father Anthony McGuire, its rector, would never tell them they have not sinned, and he hasn't too much immediate hope that they will stop; for conversion, to him, as to the church, is not ordinarily a sudden revelation but the end of a long journey.

''I've had four years in the seminary and 20-odd years as a priest,'' he said Thursday. ''Why shouldn't it be easier for me than for them?'' Archbishop Quinn's solicitude to the homosexual community does not accord with the scornful severities that the congregation for the propagation of the faith has issued alone. But we are all of us best aware of what experience has brought us closer to. The pope came to us of hard experiences that most Americans have never had; and he was met by a bishop who watches one of his own priests dying of AIDS. That is one experience the pope has yet to suffer. He is wiser than we in countless ways, but, in just this one, Bishop Quinn may be wiser than he.