The side covers fit neatly into the gearbox casing, they do not move about on the bolts like a timing cover can. So it matters not whether you fit the output yokes (or pot joints) first.
A leaky seal after replacement usually indicates the side cover bush is worn. These are a neat fit on the output yoke when new, but when they wear the yoke can move about then the seal leaks. Grab the output yoke/ pot joint and try to move it up and down.
Cure is to remove the side cover, cut or press the old bush out, fit a new bush to the cover, and get it set up true in a lathe and bored to fit your output flange. New bushes are all around .007" undersize in the bore.
Measure the thickness of the old cover gasket, if the new one is thicker you will need to re-shim the diff to preload the bearings correctly. Do this in car? I dunno... I've never had to.
There are 2 bush sizes- Cooper S/Minimatic only, and all the others.
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DrMini- 1970 wasaMatic 1360, Mk1S crank, 86.6HP (ATW) =~125 @ crank, 45 Dellorto (38 chokes), RE282 sprint cam, 1.5 rockers, 11.0:1 C/R.
