We have been hearing a clunking when accelerating from a complete stop and braking

I have the truck listed above diesel 6.7 Cummins. I hotshot so truck is under lots of strain! It has 127,374 miles recently the engine light came on and sounded like transmission (RPMs high but truck not going faster stopped to figure out transmission temperature was 210 never been that high. Let it cool checked fluid appeared normal. About two weeks ago boss had transmission flushed. I know I’ve heard bad idea called place they don’t change transmission filters so was thinking that’s the issue then we have been hearing a clunking when accelerating from a complete stop and braking. Now I’m learning that could be the u joint the noise is in the rear I know a bad CV joint can also make a transmission leak so I’m sure the u joint is shot. How do I know the yoke and differential and transfer case are okay? Also transmission has all symptoms of low fluid yet level appears normal? Transmission is a 69RFE.