As the owner of a '90 MX5, they are very nice gearboxes to use - a nice smooth shift.
That said, the gear ratios of my MX5 really wouldn't suit a P6. You'd need to ensure you have a suitable diff ratio as otherwise you'll quickly be frustrated with it on the motorway - I don't know how the 2000 diff ratio compares to the MX5.
I think the 6 speed boxes have lower (i.e. more revvy) gear ratios than the 5 speed, so would need an even taller diff. The 6 speed box MX5s already came with a higher diff ratio than the 5 speed to compensate, and have a similar overall ratio to the 5 speed in top gear.