Kevin, I don't know how many books you've read about The Beatles. I've been reading quite a few, and articles, interviews, etc. I'm doing it for a project that I'm working on. Anyway, there is tons of evidence that their relationship was very close. I'm going by primary sources (the Beatles themselves, close friends and associates, etc.) Starting when they first met each other, and continuing until the breakup. After the breakup, there's lots of conflicting information, so I won't even go into that here. But before that, like I said, there are many, many quotes that I could use to back up what I'm saying. Quotes from Cynthia, Julia Baird (John's step-sister), Tony Bramwell, George Martin, and Geoff Emerick, just to name a few. That's not even mentioning what John and Paul themselves have said. Of course a lot of people discount anything Paul says automatically. And John contradicted himself constantly, so we can only guess what he really thought about anything. But they have both described their relationship as being very close. Even Yoko, who seemed determined to keep John away from people who might compete with her for John's time and attention, has admitted that John loved Paul very much.
That quote you mentioned about "army buddies" needs to be seen in its context. During those years that John was frequently flogging him in the press, Paul at times, very understandably, began to question the relationship himself, thinking that maybe John had never really cared much for him. After John died, Yoko and May Pang reassured him that John really had loved him. We can only guess why John said some of the things he said. I bet he didn't even know himself. Their friendship definitely had its problems, but that doesn't mean they weren't close, at least at one time.