In the Pearl Harbor speech FDR lists different places where the Japanese attacked. He also mentions ships being torpedoed between San Francisco and Honolulu. What were these ships and why they get a special mention in the speech?
FDR's speech was mostly accurate. The IJN did dispatch twenty-three submarines to assist the attack. Some of these submarines were motherships for midget submarines that were to penetrate into the harbor while some were to act as surveillance prior to the attack. But the general plan for the submarines was that they were to blockade Hawaii and attack American shipping immediately after the air raid.
The submarines achieved relatively little for all their numbers. Their only success between the air raid and FDR's speech was I-26's attack on the SS Cynthia Olson which sank the lumber freighter on the morning of 7 December some 900 miles NE of Hawaii. I-69 made an abortive attack on a USN destroyer on the night of 7 December which failed and led to her depth charging. Other submarines claimed to make torpedo attacks in this time, but they achieved nothing of note.
Cynthia Olson aside, this is not to say that American shipping between Hawaii and California did not report torpedo attacks and FDR was being disingenuous. The fog of war and general post-Pearl jitters may have created an impression of more submarines and torpedo attacks than there were in reality. But the IJN really did not begin to order its submarines to take up a blockade of the West Coast until around 14 December. They might have taken up positions earlier, but a large number of IJN subs got caught up in wild goose chases to find the carriers that were absent at Pearl on 7 December. I-6's 9 December report of a Lexington-class carrier threw what was an already convoluted and overly-complicated patrol line into disarray. The West Coast blockade got to a slightly later start and achieved meager results. The IJN submarines off the West Coast only sank five cargo ships between late 1941 and early 1942 and shelled a few American shore installations. Although this created a degree of panic among Americans, it was not a terribly aggressive submarine blockade.