2007 f150 4x4 Lariat.
I just changed my rear diff pinion seal. I realigned the large nut that held the flange to match how it came off. 5 threads and marks aligned.
But, between the flange and the shaft where the U-Joint is mounted I lost my alignment…maybe. The edges match up to where you can’t tell I took it off. I’d suspect you’d see the edges where clean surface met old rusted.

My question is, what would I experience if this makes a difference? I think I have a slight sound when braking, but I could just be paranoid. I’ve read it makes no difference with these two points. And others that say it does. This is the area where the flange and union meet I’m talking about.

Not my truck internet image.

 

If you can't see your mark, just go with it.
If you feel a vibration you can always go back under and move the drive shaft. Mark it and rotate it and try it again if needed.
I know it's best to have put it back the way it came off, but you're not the first to do it.

 

Turns out I did line them up correct. Found them. Now another question. If my marks on the nut and flange lined up, plus the number of threads exposed on the spline are the same, how then can I set a torque on it? What if that moves my nut marks? Some other people are talking about a crush…washer/ ring I think. I’ve seen this on a Honda oil pan. Never seen a video that explained this in a pinion seal change.

 

Sorry, more info. Now I have a rubbing sound when slowing down. Brakes or not.

 

This is what I have from my 2013 manual. Maybe it will help.
I have never done one, so I don't have an answer for you.