It sounds like you had an awful flight. I would definitely send a letter to JL.
For what it's worth, I've flown JL F a fair number of times over the past few years, and I've had nothing but perfect service. At times, I've felt the Japanese FAs actually went out of their way to make me, often the only caucasian, welcome.
Also, JL does not do a pre-departure drink while on the ground, even in F. That is standard, so don't let that part of the experience upset you.