Water in rear- best way to flush

Just to recap I found water in the back rear of the truck that I'm putting together. These rears sat for awhile and water came in through the Breather vent. The bearings were all fine I put a camera in there and inspected it everything was fine

After I installed the new seals Cams brakes the whole thing, before I put the axle in I put a magnet with a long end into the tube on the side with that leaking breather. I pulled out quite a bit of rust and I kept going with the magnet until there was nothing left. The magnet was not long enough to reach all the way to the pinion, but I think most of that rust accumulated in that lip behind the spindle.

So I just wanted some advice on the best way to flush this. I'm going to put regular gear oil in first before I put the synthetic.

So my question is

1) should I run it with the regular gear oil for a short period of a Time drain it and then refill again with the regular gear oil run that and then put the synthetic in?

2) Or should I fill it with the regular gear oil, swap plugs and see what's on there and when I get to where nothing's on the plug just refill with synthetic? Will the plug catch most of that rust if there's any in there as it circulates and then sits?

3) Also, I don't want to pull the hubs again. I'm sure there will be some of the regular gear oil left in the hub even if I pull the axle out and let the tube drain. Will that be okay to mix with the synthetic and not cause any problems to leave it in there for the recommended oil change interval?

How would you proceed and what time frame would you use for the initial drain?