First things first, is your CEL on? Any codes, P0700 perhaps?
If there's no popping sucking blowing at the intake then your rockers are most likely (note that I didn't say absolutely) fine.
If a cam was even 1 tooth off it would have destroyed them by now as I'm assuming you've started it and driven it around.
I would imagine, from pictures I've seen and from what I experienced myself that the vast majority of your issue is due to your EGR valve. I would imagine your MAF sensor looks like a tar bunny and your intake doesn't look any better and that is probably causing a vast majority of the issues you are experiencing.
Timing being off is immediately noticeable and you would know by now if they didn't get it right at the shop.
I know the YouTube video allowed me to get mine done in my garage and that's all I'm going to say about it,
it worked fine.
You can download a copy of the service manual and the parts fiche at Sir Sam's website, I believe it's linked in the Noob Guide post at the top of the forum.
Your fuel pump isn't timed, per se, but it's optimal that it is set up correctly (3 o'clock IIRC) if it's not, you will lose ~1-3% efficiency.
Your crank being out would be bad, but if they followed the directions it shouldn't be. You can check your timing
without disassembling everything very easily with the cam pins and the flex plate pin if you are seriously that concerned about the crank being off.
If you have a leaking fuel head, changing out the filter isn't going to change that, it's the FUEL HEAD, not the filter that's leaking air.
Upgrade to a 2nd gen fuel head (You will know it's 2nd gen because it will come with wires to change the connector on the right side of the fuel head as you face it.)
Again, these are just my

but I've dealt with a lot of these issues as well.