As far as the BMS handling the new cells, as long as the voltage range covers the car's voltage range, they should work. The i-MiEV charges the cells to 4.1 volts per cell, though I'm not sure where it bottoms out before shutting down. The new cells should have a very similar charge/discharge curve, and the voltage range for most lithium batteries is quite similar, so the car shouldn't see much of a difference between LEV50 cells and bricks of 18650's, except that the new cells can take on more energy. I would be interested to see how the car would handle having much more storage available and trying to access it.
As for replacing one or two LEV50's with 18650's, you may run into problems doing that. I would expect to see the same symptoms as having bad cells in an OEM pack. A total replacement, however, should work out OK, unless there's a secret kWh counter built-in.
I've read that continuous C ratings on prismatic LiFePO4 batteries is 3C, with a burst rating of 10C. 6 amps on the 18650's would be 2C, 30 cells in parallel is 180 amps as Don stated. So for the whole pack, 180 amps at 360 volts is 64.8 kW, more than plenty for the i-MiEV. Even at 330 volts, that's 59.4 kW, still more than the i-MiEV requires. The LEV50 cells hit 3C at full acceleration.
The battery pack would be increased from 50 Ah (16 kWh) to 93 Ah (29.8 kWh), for a range increase from 62 miles to 115 miles per charge.