When I converted my Commando motor into my Featherbed frame I made the engine plates for it with my motor leaning forward, when I need to remove the motor I just undo all the top head stay and remove the carbies then undo the 4 engine mount bolts and lift the whole motor, gearbox, primary and bottom engine plates all in one go, the same as when I am installing the motor I have all engine mounts bolted to the motor, gearbox and primary with the engine on the mounts tighten up to the motor, lift it over to the frame slid it in on a angle and when near position just let the motor and mounts drop into position, it just drops in the right place from the weight of everything and just put the engine mount bolts to the frame.
You might have to use a ply bar just to line up the frame holes but mine just drops into the right position every time, on the top front and rear through bolts I have a steel spacer that sits inbetween the frame lugs this is to stop the lugs from bending if you over thighten the engine mounts the two bottom lugs at the rear has 2 seprate bolts.
I am sure the Atlas motor would be the same to lift in position with everything bolted up to the engine plates, I be doing the same when I finaly do my Manxman project.
Ashley