Will an auto tranny from a 2000 outback work in my 99 outback

Yes. Both are phase 2. Confirm that they have the same final drive ratio by the trans numbers in front of the starter. (They should be. Both came standard with 4.44 but always double check.)

Be aware that both the 99 & 00 were prone to the "delayed forward engagement" problem on some automatic transmissions. Using Trans-X fixes the problem.

What about the difference in the shifter itself. The 99 pulls straight back and the 2000 has the staggered shift

Never had an issue with it. I put an 01 trans into a 99 and it was a direct swap.

Do I need to switch the shifter inside the car also