I'm gonna go ahead and toss this out here. Jujitsu. If a samurai saw someone walking about in a suit of Knights armor, he would toss them on the floor. No need for to draw his weapon.
There is also the rifle, arquebus I believe its spelled. Can he use that instead of the yumi?
Give the samurai a kanabo to have a 'fair' contest, but his two arrow shots would just go into the eyes anyways. (Watch Deadliest Warrior, Samurai vs Viking for the arrow shot example). I think this is a better match up because both of the warriors were in societies where training began at a very early age. This is the most important factor - training. They put the stats all into a simulation, the samurai won against the Viking but barely (it was 55 to 45 I think). Personally I would put my money on the Viking in that case...
The kite shield is probably a tactical error one on one (due to the fact it is strapped to the arm - you figure out why this could be a disadvantage)