You are mistaken though when it comes to the range of the bombers and the targets:

“After Nagasaki was bombed, Japan had nine large cities (populations over 100,000) that had not been bombed. They were Kyoto (1,089,726), Sapporo (206,103), Hakodate (203,862), Yokosuka (193,358), Kanazawa (186,297), Kokura (173,639), Otaru (164,282), Niigata (150,903), and Fuse (134,724) [Figures are for 1944 from Japan Statistical Yearbook]. Sapporo, Hakodate, and Otaru were on the northernmost island of Hokkaido and were, therefore, beyond the range of U.S. bombers operating from Tinian Island. So six targets were available. US Secretary of War Henry L. Stimson had removed Kyoto from the target list because of its religious and cultural importance. So five targets were available. Compared with the number of cities that already lay in ruins, five more would have been, well, small potatoes. Of course, it would have been possible to re-bomb some cities that had already been bombed, but on average these were already 50% destroyed.”

Sapporo, Hakodate and Otaru could all be reached by the B-29s operating out of Tinian: http://www.history.army.mil/books/wwii/MacArthur%20Reports/MacArthur%20V2%20P2/Images/p_144.jpg and http://www.airforce-magazine.com/MagazineArchive/Pages/2010/April%202010/0410mission.aspx . The distance from Tinian to Sapporo is just under 2,000 miles and a B-29′s range (i.e. being able to fly out, bomb a target and come back) is listed as being over 3,000 miles. Indeed some B-29s got in trouble over Japan and had to make emergency landings in the USSR (which would be further than flying to Hokkaido), where they were reverse engineered as the Tu-4 (much to Tupolev’s displeasure since he designed aircraft for a living and loathed the idea of being ordered to copy an existing aircraft) and then returned to the USA. The crewmen were interned since the USSR was neutral in the war against Japan at the time and Stalin wasn’t about to give the Japanese a reason to start hostilities before he finished with Germany (although the USSR did allow the US airmen to “escape” into Iran which was being occupied by the Soviets, British and Americans at the time, whereupon they returned to the USA).

And Sapporo was indeed considered as a target. The original targets under consideration in April 1945 were Tokyo Bay (for a non-lethal demonstration), Yokohama, Nagoya, Osaka, Kobe, Hiroshima, Kokura, Fukuoka, Nagasaki, and Sasebo. A number of these were scratched since they had already been burnt to the ground. Then in May the list under consideration was (in order): Kyoto, Hiroshima, Yokohama, the Kokura Arsenal and Niigata with the Emperor’s Palace discussed as a possible target but rejected. This list was then narrowed down to Kyoto, Hiroshima, Yokohama and Kokura Arsenal with Niigata under consideration. At the end of May this list is then narrowed down to Kyoto, Hiroshima, and Niigata. A couple days later Stimson rules out Kyoto as a target. By late July the target list is Hiroshima, Kokura, and Niigata. Nagasaki is then added as the final target in the list.

For the missions themselves Hiroshima was the primary target and Kokura the secondary in case Hiroshima couldn’t be bombed. After Hiroshima was bombed the next target was Kokura as the primary target and Nagasaki as the secondary target. So were it not for clear skies over Hiroshima and cloudy ones over Kokura the Kokura would definitely have been bombed at some point by August 9.

Now according to Richard B. Frank in his book Downfall (p. 303) after the bombing of Nagasaki the commanders in the Pacific made their own recommendations on targets for future weapons. Specifically, Admiral Nimitz, General Carl Spaatz (commander of the United States Strategic Army Strategic Air Forces in the Pacific) and General Nathan Twining (commander of Twentieth Air Force, formerly XXI Bomber Command, based on the Marianas and containing the B-29s on the islands including those of the 509th Composite Group tasked with dropping the atomic bombs) met with General Farrell and Captain Parsons (both of who were on the Target Committee for the atomic bomb). By the afternoon of August 9 all of these folks were urging Washington to review the target lists in light of the bombs so far having “far exceeded optimistic expectations”. On August 14, General Twining submitted a new list of six targets (in order): Sapporo, Hakodate, Oyabu, Yokosuka, Osaka and Nagoya.

As for the source of the fissile material, I suspect it was increasing capacity at K25 which was just starting to come online at that time.