No. The 2000 GT was a 4.6L that has a different bolt pattern than the 90 5.0L. You would need an auto trans from a foxbody or 94/95 5.0 or you could use an auto from a 94-04 V6 car. The 3.8 has the same engine pattern as the 5.0. I am pretty sure that in 99-04 a V6 auto and a V8 auto were the same trans, just different bellhousing pattern.
One thing to research is the flexplate. I am not sure the tooth count of the V6 and a V8. I know with a manual you could use the V6 bell housing on a V8 and it would bolt up but the flywheels are different size (157 tooth for V8 vs 164 tooth for V6) so you end up with a starter location issue.