I went through similar research on my father over the past 10 years. It is often a long road, but don't give up!
The best way to find out where the ships were is to write to the national archives (email@example.com) and ask them for a copy of the Movement Card for the ships you are interested in. When you e-mail, be sure to include as much information as possible on the ship you are looking for, as there were often two ships with the same or similar names.
The movement card was kept for each merchant ship, and lists the dates and ports of departure and arrival.
The archives often charges for copies of this stuff. Here's a hint - ask for one or two ships at a time, and they will probably mail them to you free. The movement cards are usually only 2 or 3 pages, and they don't bother charging for something that small.
Be sure to include your name, address and phone number. Sometimes if there are confusing records, they may call you and try to clarify what you want.
Now that I told you that, I'll save you some trouble :-)
I have some information on the Frederick Lykes. The dates are a bit confusing though. Lykes left Capetown, South Africa on June 30, 1942, arriving in Baltimore on July 12. Since your Father's records say he was assigned to Lykes on the 8th of July, he may have been allocated to her prior to her return to the US. in any event, she left Baltimore for Africa (not sure of the port) on July 24, and arrived back in New York on August 20.
The Permian was in New York on January 16, 1943, and left for Halifax, Nova Scotia on January 24, as part of convoy SC-118 (SC-118 went on to Liverpool, England, but Permian went only as far as Halifax), arriving in Halifax on January 27. She left Halifax on January 31, joining with convoy ON-160 (which had originated in Liverpool), arriving back in New York on February 4.
The James J. Hill Left Baltimore for Hampton Roads, VA on January 18, 1944. She left Hampton Roads on January 25 for Oran (Algeria) as part of convoy UGS-31, arriving in Oran on February 12. She left Oran on February 24 as part of convoy GUS-31, arriving in Philadelphia on March 18. She remained in Philadelphia until April 1, but your father left her just before her next trip.
Most of the rest of this would take some digging to sort out. Note that "Norfold" should be "Norfolk". Not uncommon for these documents to have typos! Regarding Coxswain and Boatswain, you can find tons of info on these "Rates" (job classifications) by just Googling the words.
Abatu is in Japan, on the Island of Hokkaido, near Sapporo. My guess is that he was assigned to some activity in Japan after the war ended, and that could relate to the dates for out of the country and back into the country. He may not have been assigned to a ship at that time. Many jobs were needed on shore stations, so it is pretty common to find periods where a sailor was not assigned to a ship.
If you haven't done so already, you should request a complete copy of his service records from the National Personnel Records Center. This is free, but sometimes takes months to receive. More info at: http://www.archives.gov/veterans/evetrecs/index.html
If requesting, be sure to ask for the complete personnel file in the comments box in the on-line form. Otherwise, they will only send you the discharge form (DD-214). Don't be surprised in there are big gaps in the records. Much information during the war got mis-filed, or never filed. It was a chaotic time, for sure.
Hope this helps you on your way. If you have more questions, be sure to ask, and someone will always try to help if possible. You can contact me directly (firstname.lastname@example.org) if you have specific questions. I am always ready to help.