OK some more time to post up some photos 
This is just one Gearbox Case as found;-
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and a Random typical Transfer Housing, not run with the above Gearbox Case, however, the issue is fairly evident;-
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Although I've been fitting the Tapered Roller Conversion, that's fine for the Idler Gear, however, the Outrigger Bearing on the Input Gear needed to also be looked after and although the Idlers now run on a dead shaft, they still needed to be 'in the ball park' to ensure the Gear is square in the whole train, so to correct this, Dummy Shafts are loaded in to the Gearcase;-
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Then mounted & clocked up in the Mill;-
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Fit the Transfer Housing and Clock up again;-
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This was the best set I'd come across, the and even then the error (as shown in the X & Y displays in 0.01 mm);-
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This was another, and just after taking an initial cut, you can see the error here;-
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What I do at this point is to clock back to the Gearcase Dowel Centres, and re-bore the dowel holes in the Transfer Case, to put them back on to the Gearcase, Make some new Dowels, the originals are stepped, with 7/16 in the Gearbox Case and 3/8" in the Transfer Housing, so I make mine 7/16" right through now.