Marking driveshaft flanges when replacing entire rear axle?

I am replacing the rear axle assembly on my 2001 4Runner 4WD. The FSM states to place matchmarks on the propeller shaft and rear differential flanges when removing the drive shaft. I have always assumed this was for balance/ vibration issues. What about when you replace the entire rear axle housing assembly? What do you match it to on the new differential flange?
 
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I've swapped driveshafts and rear axles a few times and the only things I paid attention to was keeping the driveshafts in phase and torquing everything correctly. You only need to worry about phasing if, during the swap, your rear driveshaft has separated from the slip yoke.

Driveshaft phase is probably easier described by a google search than me trying to ham-fist my way through a non-technical description.
 
I am going to be replacing the whole rear axle shortly too. Its balanced pretty well from the factory, but changes can occur due to wear. This is why they want you to replace as it comes off. Since a different rear axle did not wear with what you have it is really a crapshoot when you put it together. Best you can do is adjust it after the fact if you have vibration problems. When I changed out the driveshaft and transmission on mine I had no problems with any vibration even though they were never matched up
 
This is right:

I've swapped driveshafts and rear axles a few times and the only things I paid attention to was keeping the driveshafts in phase and torquing everything correctly. You only need to worry about phasing if, during the swap, your rear driveshaft has separated from the slip yoke.

Driveshaft phase is probably easier described by a google search than me trying to ham-fist my way through a non-technical description.

I have dealt with many drive shafts and I do not worry about its original position other than the phasing:
 
Thanks, I plan on only unbolting the driveshaft from the rear. Hopefully this will not cause any issues.

use paint mark the flanges front rear .. put new shaft in with the front rear marks in the same position. block wheels e brake on put in neutral so it bolts up , comes out , goes in easy.

if it vibs reverse the install .. if it still vibs bring to axle balancing shop it can happen..
 

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