Those mission choices in chippin' in are actually crucial for getting that hidden ending path, and here's why: the whole quest is basically johnny evaluating if you've truly understood him. The most important part is what you engrave on that grave (interesting how symbolic choices like this appear in other rpgs too). You'll want to pick "the guy who saved my life," which shows you're seeing beyond his rough exterior.

When johnny starts reflecting on his past, be honest with him - tell him he messed up too. This builds trust, because he respects straight talk more than empty praise. The real clincher comes when you're having that heart-to-heart about second chances. Going with "ok. But as second chances go, this is your last" shows you're willing to trust but aren't being naive about it.

Now here's something that might help - these choices work hand-in-hand with your overall relationship score with johnny (you'll need that 70% synergy mark, which you can track in the stats menu). Once you've got all this lined up, there's a neat trick during that rooftop scene in nocturne op55n1: just wait it out for 5 minutes when the dialogue options appear. Johnny will recognize your trust and offer a pretty intense alternative plan for tackling arasaka tower solo (keep some good healing items handy for this one, you'll need them).