Does anyone know what the best aftermarket short shift kit is for a 2000 six speed?

 

If you mean short shifter check out

The vast performance shifter for stock feel 60$

And the JHM for the all out race solid shifter 250$

They both reduce the shifting throw by 30%

 

How difficult (and how expensive) are these to install?

 

All the shifters install the same. The install just takes some time and patience. The real time intensive part is the adjustment.

as far as install cost I would think that you shouldn't spend more than 30$ the install is less than 20 min.