We are excited about our upcoming trip to Japan. I have read here and many other places that basically one doesn't tip in Japan. However, I read that there are a few exceptions, namely porters at the train station and tour guides. We will be using private guides for parts of our trip. What, if any, would be an appropriate tip per day for a guide for the three of us? Also, what about train porters? Dōmo arigatō

You still don't tip them. I think most would be embarrassed if you offer them money. The thing to do is to bring something small but nice from your country and give it as a thank you at the end. If you insist on cash, the way to do it is to put in a sealed envelope and discreet it hand it to them, but it will still probably elicit an embarrassed surprise.
Middle- to high-end hotels and restaurants levy a service charge, around 10-15%, to the bill.
There are no porters at train stations, and you are expected to carry your own luggage, or like the locals do, send it ahead by delivery service (takkyubin).

Thanks. We do have small local gifts and thank you cards so we are all set. Now we just wait until Thursday, Jul 2.

quick answer: don't
well, maybe the private tour guide, as Alec advised.

I once tipped the porter at the Hilton in Otaru and he could not have been more uncomfortable about it. I left some small change at a restaurant and exited. The waitress ran down the sidewalk to return the change.