The slip joint goes closest to the transfer case.
Don't go to the hardware store to buy the bolts as they must be high tensile and you are unlikely to get the exact size. They will be the same size as the bolts in the front prop shaft.
The main fluid level is below the level of the seal. You may get a very slight leak from any oil trapped up near the flange, but you should not need to top up any oil.
A new seal will be a good idea with the new flange.
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