I have 2000 ford ranger xlt 3.0 m/t, i recently changed the transmission fluid with the merc atf that is used for the trans after, the fluid that was in the trans was a bit black with hints of red, so it wasn't terrible but after that my transmission has been making a weird knocking noise near the end of the trans, right before it connects to the drive shaft, it only happens if the truck is rolled to a specific position

For example, i park and i stop the truck i wont hear the noise but if i roll back a slight bit and the stop i begin the hear the noise again

idk if its a output shaft bearing
I also just chnaged the motor mounts incase it was just that
But nothing has changed

 

Welcome to the forum

The drive shaft will have a slip joint or slip yoke, it allows the drive shaft to get shorter or longer as rear axle goes up and down
Try lubing it

 

Ill try that i have one more question does a m50d-r1 transmission from a 4cly work on a 3.0

 

No, M5OD-R1(M5R1) is just a model number, like Ranger is a Ford Model, doesn't tell you if its 2WD or 4x4 or regular cab or super cab, for example

M5R1s have integrated bell housings, not removable, and since the bell housing has to bolt to the engine the engines bolt pattern matters
And 2WD and 4x4 versions, they are different

M5R1s came in 4 different patterns, and 2 versions for 3 of those patterns, i.e. 2WD or 4WD
2.0l, 2.3l, 2.5l SOHC pattern(1983-2000), 2WD and 4WD
2.3l DOHC pattern(2001-2011), only 2WD
3.0l OHV pattern(1991-2008), 2WD and 4WD
2.8l, 2.9l, 4.0l OHV and SOHC pattern(1983-2011), 2WD and 4WD

Of the 4 patterns none are interchangeable
And there are 7 sub-model versions when you include 2WD and 4WD