I had been wondering what had happened to you

[EngLearner]

John hasn't seen Peter for a long time. He bumps into Peter on the street, and the following dialog takes place between them:

John: "Hey! it's been a while since we last talked. How have you been?"
Peter: "Yeah, sorry about that. I've had some family stuff going on."
John: "I had been wondering what had happened to you. Is everything okay?"
Peter: "Yeah, everything's fine. Thanks for checking in."

I made up the above dialog. Did I use the bolded tenses correctly?

 

[emsr2d2]

John hasn't seen Peter for a long time. He bumps into Peter on the street, and the following dialog takes place between them:

John: Hey! It's been a while since we last talked. How have you been?
Peter: Yeah, sorry about that. I've had some family stuff going on.
John: I had been wondering what had happened to you. Is everything okay?
Peter: Yeah, everything's fine. Thanks for checking in.

I made up the above dialog. Did I use the bolded tenses correctly?

Note my capitalisation correction in John's first line. Always use a capital letter after any closing punctuation mark.

The tense you've used is grammatical but you'll also hear "I was wondering what ...".

Your dialogue is quite formal for a conversation between two friends. At the very least, John's second line would open with the contraction "I'd been".
I'm not necessarily suggesting you try to replicate it, but here's how the dialogue might go in very casual British English:

John: Hiya! It's been ages! You all right?
Peter: Yeah, it's been yonks. Sorry. Had some family stuff going on.
John: Ohhh. I was wondering what was up. All good?
Peter: Yep. All fine now, ta.

 

[EngLearner]

If I use "I was wondering" at the beginning:

1. I was wondering what had happened to you. Is everything okay?
2. I was wondering what happened to you. Is everything okay?

Can either version be said in the dialog in post #1?

 

[emsr2d2]

They're both possible but #1 is more likely. Whatever might or might not have happened happened before the wondering.