From looking at the first part of the tutorial related to the link you posted for the second part, you will be receiving some token from the app that it gets from the Apple server after registering for push notifications. Your app then sends that to your server (with whatever other information you need). Then you use that token when you send pushes to the Apple server (in response to stuff happening in your app, I assume).
It has a lot of good information about setting stuff up for Pushing. I've not looked into it because I don't see using it any time soon.
It does seem to indicate that the specific SSL certificate required to be used is generated by Apple. But I still haven't been able to figure out how you get it to your server. As best as I can tell, once you generate it on your Mac and create the .pem files, you will need to upload some or all of those bits to your server. Probably to the same directory as your PHP scripts.
I tested the bits for telneting to the APNS on my Mac Mini and got through. Then I tested on my JagPC VPS and could not. But that is probably because I don't have port 2195 open (I keep my VPS very tight).
I suspect the upshot is that I think you will need to go the VPS route. If you do, you can request that JagPC make sure that the needed ports are open from the beginning. They will help you move your hosting account to a VPS free of charge. This means that everything you have on your hosting account will be on the VPS (email accounts, database and such).
Following some links in the tutorial, it looks like you need to make sure that JagPC opens ports 5223 and 2195 for your use. But I would not be surprised if they do have an issue with that on a shared hosting account. It might be that you have no choice but to get a VPS (where you control the ports).
And, it does look like there will be things that need to be done at the command line level on your server. This would require a VPS or better.
What I don't see in AppGameKit is how you actually receive and process push notifications. There are only two commands related to setting up and getting the token to send to your server.
I'm not sure I am being very helpful here.
Cheers,
Ancient Lady
AGK Community Tester and AppGameKit Master