Hmmm. I didn't even know the Vatican Museums were open before 9. But, you will certainly have no problem getting to the port for your sailing. The train takes about 1:20 min and there is at least one train per hour. The Civitavecchia train station is about 4 long blocks from the entrance to the large port, and there is a free shuttle bus that runs from the entrance to the pier. A more convenient option is to get a taxi from the station to the pier, but you cannot count on a taxi being at the station (its hit or miss). I am not positve about the current train cost, but one-way should be about $10. Most of the trains are locals that require no reservations, They also have some very nice "IC" trains that make the trip in about 45 minutes, but these trains cost more (10 1/2 Euros for 2nd class)and advance reservations. Since you didn't mention your hotel I cannot help with the timing, but you would probably not need to catch a train to the port until as late as 3.