Why did japan begin a conflict with russia?

Ok the reason are somewhat complex. There was a prolonged dispute regarding Korea and Manchuria. 
Ostensibly, China had leased Port Arthur in Manchuria to Russia which provided Russia its only year-round warm water port in the Pacific. However, the Japanese had also occupied Manchuria and Korea and did not like European influence in the region, perceiving it as a threat. Of course Japan was also an imperial power in the region. Germany, the USA, Russia, Japan, Britain, Austria, British India,Italy...had all repressed and fought against the Chines Boxer Rebellion around 1904. Japan wanted Russia out because it saw the Trans-Siberia railroad being built and extending to Manchuria so that Russia's holdings there could be quickly militarily supported. 

Nicholas II argueably was incompetent and went 4 mos. failing to answe Japanese demands regarding Russia's movement out of Manchuria. If one accepts that version, then one can yet again blame the autocratic Tsar for failing to respond in a timely manner as hid advisors were encouraging. The Japanese attacked Port Arthur. The Russian put up a good fight on land and at sea but were ultimately decimated. About 120,000 people were lost on each side. Japan gain world recognition as a new superpower. Russia's repuatation as a superpower suffered so much that iy changed Germany's view of Russia which would affect Germany's regard for Russia in WW1 and WW2. The British argueably provided the Japanese the intel.used to defeat the Russians, and had signed a to 
fight as an ally of Japan if necessary to win the war in Asia. 

While Japan clearly won the War, it also set up a military mindset and set of military condition that would later harm all nations involved. It did much to foment the Russian revolention. It did much to foment Japanese imperialism and to encourage Germany's military build-up prior to WW1 and to regard Russia in a way that underestimated actuall Russian military capabilities. It also encouraged British imperialism and seduced the US into negotiating and policing such conflicts. China of course continued to suffer, but China's fate was spelled out as one in need of radical change. 

In WW2, when Japan attacked Russia, the Russian forces overwhelmingly defeated the Japanese forces and retook by the end of the war much of the land it lost to Japan in the 1905 War.