To remove the carbon, simply carefully rotate the crankshaft to position that piston at the very top, then scrape the carbon off with a piece of sharp wood. This is the safest way. Any scratches that a metal tool might leave will weaken the piston.
Don't worry about the timing. The gas engines are super simple to time. You will simply rotate the crankshaft to the TDC mark and line up the cam sprocket mark. They probably told you to mark it, because for some operations you might not have to turn the cam or the engine. For a head removal you only need to align everything when going back together.
After getting the head back on, be very careful in tightening down the camshaft. First of all, get the cam in proper timing position, so valves will not contact pistons. If you tighten a bolt or bolts at one cam bearing journal, you can easily strip the aluminum bolt holes and even break the cam. Lay the cam in place, time it and get all the bolts started, then tighten down evenly by tightening each bolt only about one turn at a time.
My engine does not have an EGR valve on the exhaust manifolds, so I have no experience with that, sorry.
When you start back together, think things through and take your time. As an example, not tightening the cam bolts down gradually as I talked about above could cause damage, also tightening them without the engine and cam timed could cause damage. Use your head and be patient while putting it back together.
Also, have you found out how you're supposed to "angle torque" the head bolts? Make sure you know the drill and have a really good breakover bar. You will think you are damaging the bolts when you do this. Also, when you get ready to torque the head bolts, make sure you don't have a time constraint and your head is in the job. You have to torque in sequence, then go around and angle torque in sequence. This is not a good time for an interruption. You should plan on doing this all in one session.