Explaining the Catholic Church to an atheist

I have been having a discussion on a local forum about belief in God. As far as I can tell, I seem to be the only one who is an out-of-the-closet theist. There may be others lurking, but no one else posting apart from me.
It's a very small neighbourhood forum , but nonetheless it's interesting that the overwhelming concensus appears to be agnostic/atheist.
There was one Christian called Laurence who posted for a while. But we tangled a bit over doctrinal issues ( I felt that he just couldn't help taking side swipes at the Catholic church, even when he thought he was being reasonable) and I think I got the better of him and he seems to have decided to lie doggo for a while.
In all honesty, I think that's probably a good thing because he really was inclined to be a bit of a cartoon fundie and grist to the atheist mill. He spoke in the lingo that felt completely normal to him but often sounded quite alienating and patronising to anyone outside that milieu. As a consequence, some of the responses he elicited were quite sharp put downs and then he'd get huffy, and the conversations that ensued tended to generate more heat than light.
Anyway, he seems to be taking a back seat for a while, so I'm the resident Christian.
That suits me fine.
I have the 'joie de combat' and I enjoy a fesity back and forth, and tend to feel more exhilarated than wounded by the opposition. I think it's been good for me to cut my teeth ( apologetically speaking) in this way, on a small forum, but one where the people are mostly known and therefore tend to be a bit more accountable for their words.

It's a very local forum and they meet up fairly frequently in local pubs. Although I've only gone along once, I've met a few of them and will be going again in a few weeks time.
The most recent discussion has been about belief in God, but it's just about to morph into a discussion about the Catholic Church in particular, and the rather audacious claims that she makes regarding herself.

I thought I'd make copies here of the conversation as it unfolds from this point.
If anyone is interested in reading the earlier parts of the conversation you can find that by clicking here which is where it starts.

Al is  a pretty conscientious secularist, friendly with Keith Porteous-Woods and Terry Sanderson of the National Secular Society and was very supportive of the "Protest the Pope" campaign just prior to the Papal visit last year. 
I like him very much and I can appreciate that most of his objections to religion in general, and to the Catholic church in particular, are grounded in a rather noble ethical perspective. Nonetheless, I believe he is quite mistaken about the Catholic church, and I hope that I can begin to show him reasons that will lead him to reconsider his opposition.
His objection reminds me of Archbishop Fulton Sheens observation that "there are not a hundred people in America who hate the Catholic Church. There are millions of people who hate what they wrongly believe to be the Catholic Church — which is, of course, quite a different thing."

So here's the comment  I made that Al took issue with:

The concept of being a bible believing christian without an authoritative church doesn't stack up at all.
A bible only christian runs into the sand very quickly when he tries to maintain an infallible bible without an authoritative church.
You can't squeeze infallible bible juice out of a fallible catholic orange.
The church came before the bible. The early christians weren't wandering around with a bible tucked under their arms going off to bible study groups on wednesday evening.
The early church was Jewish and the Jewishness of Christianity is still very present in catholicism and in the catholic mass.
That is not the case in 21st century nu church which tends to revolve around a stirring sermon and worship songs.
That is the short answer, but I will try to put more flesh on the bones later.

Al responded:

I have as much difficulty with this as I do with bible-believing Christians of the fundamentalist persuasion. If I believe in anything it is the need for critical thinking, the necessity of questioning authority and orthodoxy, so the concept of an 'authoritative church' that includes a Pope who can be 'infallible' is, for me, well beyond the pale. And I don't want to get into a slanging match about your church, but with things like the Inquisition in its history, its record is a long way from impeccable and so I would have thought its 'authority' has simply not been earned.

I wrestled a bit with how to answer him. Not because I was stumped ( ha! as if!) but because I was a bit daunted by even beginning to answer.
There is simply so much to say and so many ways to say it.
I posted a question on an email list I belong to ( The Catholic Spitfire Grill) and asked for some thoughts about how I could answer this in a way that would make sense to an atheist.
I think that part of the problem I was having is that the question of the churches authority, presupposes a belief in God.
I'm quite used to having a discussion like this with other Christians, but Al doesn't believe in God.
The conversation was moving away from answering questions about the existence of God, and why theists are well within their rational rights, to specifically defending the Catholic Church and her claims to be a divine institution.
That felt a little strange to me, as I could see that, without believing in God to begin with, that could all easily sound deeply potty.
I got a couple of answers from the Spitfire Grill that really helped kick me off in the right direction.
In the next post I'll talk about how I responded to Al,
And meanwhile,I'd really like to hear any thoughts that anyone else has about how they would answer a question like this, and especially if there are any points that you think ought to be included!