By lowering the A unit bodies with washers, it dropped it right down on top of the pilot. No spacer needed between the body and the pilot. It does need a .040" spacer between the frame and pilots when it's mounted, just because the frame is recessed that much in the shell as you stated earlier. Body mounted steps, and a custom coupler mount for the rear of this thing and it will be time for paint touch ups and the rails. 
This is the trailing unit, 19C, so I left the coupler stick out a little further than it should so there's more clearance when coupled to its train. The leader, 19L, will get it's coupler set back in further for better appearance.
The interior was painted tan because Lionel had it painted red from in factory. Cab lights were removed because I hate running with the lights on inside, and the smoke unit was modified and rebuilt with new batting. Still need to add all the correct length MU hoses to the rear of all the units because Lionel included the stubbies with this set. They are in the trash now.
