Japan was starving in 1945 OTL and still prepared to resist.Errr... otl we took the shortcut of dropping 2 Abombs, but isolate and starve would have worked just fine.
The two basics that will be hit hard are oil and transportation. Oil for obvious reasons. Japan has plenty of coal, but as it becomes more difficult to run an air defense, the rail network will get hit. That will make life in the cities problematic because you can't feed them. You run into the side issue of how to get aircraft over Japan, but it will happen eventually.
The problem is eventually the situation will stabilize and normalize. The European war will have to be completed before Japan can be dealt with. People will go back to their villages. Invasion sites are obvious. Weapons, bunkers etc will be prepared and hidden. There will be lots of hunger, lots of dead, but you can't bomb everything so there will be a lot of fanatics left with a lot of weapons willing to keep the gaijin off the home islands at any cost. Essentially a North Korea situation.