Japan technically didn't win the war against Russia. Japanese economy nearly broke and the Russians just "lost" because Nicholas II didn't see any reason to continue the war. The fact that the peace negotiations were headed and conducted by russians diplomats was not a coincidence.
The Japanese had suffered severe losses, but the Russian pacific fleets and the east sea fleet were destroyed, and the Japanese managed to occupy Port Arthur. Any attempt to relieve the siege by the Russians were beaten back - Japanese superority in artillery being a major factor for winning the land battles despite antiquated infantry tactics (the Russians learned faster than the Japanese that bayonet attacks against machine gun nests aren’t a great idea).
It is true that the Japanese did not enforce all demands they wanted, but their success convinced their high command to pursue further expanisionist goals, leading to the next war against China - it seems like the Japanese military command of the time did not see it as a lack of success. The Japanese fleet actually grew in numbers due to the capturing of Russian ships.