transmission replacement for a '95 3.8l with a 2000 engine

i have a 1995 3.8l mustang... when i got it i was completely unaware of the recall due to head gasket failure... unfortunately, the failure took my engine with it and a 2000 engine replaced it... 4 years later i am having to replace my tranny... my question is this: would i come out better putting in a 2000 tranny or should i find a rebuilt '95? would it matter?

any insight is greatly appreciated as the replacement will take place within the next month...

I would get a 99-04 tranny.