My 14 Gt is making A whining Noise when starting to move & Making a Clunk sound when coming to a stop. Recently replaced the pinion Seal & added new Fluid. Could Tightening The Pinion Nut be A Solution?

 

It sounds like there's too much backlash in the pinion gear so yes, it might be worth tightening the nut a little.
When replacing the pinion seal, it's a good idea to mark the position of the nut before you remove it to ensure that you tighten it to the same position afterwards.

 

I just replaced my pinion seal and got the torque wrong. It was too light. I had the whine issue as well when I backed off the gas while still in gear. The fix was going back in and setting the pinion spin to 10 inch pounds. That required about 175 ft pounds on the pinion nut. All is well now with my 06....just cleaned up after redoing the work. The counting threads and marking everything just doesn't work. The preload has to be set correctly or there will be damage. Just no shortcut to doing it right.....unless you are lucky....and I wasn't.