I2C pullup resistor calculations
There is a typo in the Atmel datasheet, the rise time for the 100kHz case should be 1000ns, not 100ns (it would not need to be lower than the 400kHz case of 300ns) then you get:

\$\dfrac{1us}{400pF} = 2.5k\Omega \$; for the 100kHz case 

The LCD datasheet (almost certainly) means the maximum bus capacitance, not the capacitance that it adds to the bus. It probably adds around 10pF. You can either check with an LCR meter or just set it up with a 2k resistor and look at the rise times.

Many devices don't fully comply with the official 400kHz specs, so it's best to refer to these for understanding the conditions under which 400kHz can work (bus capacitance, pullup/current source/etc) See section 6 onwards in particular (for example see note 4 on pg.47:


  [4] In order to drive full bus load at 400 kHz, 6 mA IOL is required at 0.6 V VOL. Parts not meeting this specification can still function, but not at 400 kHz and 400 pF)   


Further on, these tables are pretty helpful, and look to agree with your calculations: