I guess I'll chime in since I just ordered most of this stuff... I'm still in the pre-build process though, so I might not be able to answer a lot.
For one, I ordered these pilot burners Q314A4586 per another thread that I found using the same valves and thermocouples. Though to be honest, I'm not sure what the difference is between those and the ones you have listed.
The valves have 1/2" NPT threads on them and come with an adapter for 3/4" on the input side. For the output, it's also 1/2" NPT and you'll need to adapt that to however you want to hook up your burners. The orifice on the burner is (I believe) a 3/8" flare fitting. You can use flexible gas line ($$), or get a cheap flare tool and some flare nuts to use soft copper.
I can't really answer you on the regulator however as I went with natural gas.
For the PID, I don't think you'll want to use the SSR anymore. Since the PID is set up to fire the SSR in fast intervals for your heating element, your gas valve won't be happy with that. You can most likely configure your PID from SSR mode to Relay mode and use the relay to send the 24VAC from your transformer to the valve. I bought the Auber SYL-2362, which seemed pretty ideal for a gas setup like this.
I don't really think you'll need a needle valve for the pilot as you'll be running the pilot tubing from the Honeywell valve and there is a pilot adjustment screw on there. You'd really only need a needle valve if you're running your pilot straight from the supply line.