Dave,
The engines in the 1999 and 2000 are the same. Even thought they were making the 1999 cars in 1998, the 1998s are all considered to be the 1999 model due to the car design change (first year of NB.)
If you get to the right person within Mazda I think you will be able to get some type of accommodation on the repair. If you are unable to get assistance from Mazda, there are low mileage used motors that are available that can be purchased for under $1000 dollars. There are companies that sell low mileage Japanese motors also.
The labor for doing the swap will be double at a Mazda Dealership, and you might be able to get a used replacement installed for less than what a Dealer will do if you get a partial warranty accommodation from Mazda.
Good luck!