Moqtada al-Sadr's Mahdi Army fought US, Iraqi forces in Baghdad and Basra on Tuesday.
Hard-liners play tough to prevent reformist gains in March 14 vote.
Some 100 members of the Iranian antiregime group have left a holding camp in Iraq in recent weeks. Iran says amnesty offer holds.
High-level meetings are part of Admiral Keating's trip this week, following a flap over Hong Kong port visit by USS Kitty Hawk.
Iranian video shows apparently routine activity by Iranian patrol boats, while Pentagon officials say radio threat may not have been from Iranian forces.
While the US State Department demands an explanation, Iran's Foreign Ministry calls the incident 'normal.'