You are over-analyzing the shirt business. White is fine, pale blue is fine, pink is fine. white with stripes is fine...What color is your suit, or, if you just have a jacket and slacks, what color or those? What color are your shoes?
Only you know the answers to your questions, so pick a conservative color/pattern that goes with your wardrobe and you'll be fine. Any vivid colors and you will stand out - but even then, if the color matches the outfit, there is no reason to avoid them unless you are a lawyer or some other profession where a conservative wardrobe is the norm.
As for pockets and colors and buttons and sleeve styles...you might be surprised at how little your colleagues will care about such things, so get something you will be happy with and live with it. Sometimes a shirt is just a shirt, and not a definitive statement about your worth as a human being.
Finally, your size sounds very common. If something is getting lost in translation, no need to worry: there are plenty of tailors and shirt-makers here in Tokyo. Go into any men's store in a major department store and they will have fabrics to choose from, and they will measure you and let you choose from a selection of styles. You can get one made for less than $100, and it will last you a long time. In Shibuya there is a custome-made shirt store called Tailor Fields, and they used to have a special deal where you could get two shirts made for $80. If all of that is too difficult, head down to the Gap or to Banana Republic and pick it off the rack.
Good luck. And don't sweat the details.