hi,
I will try to answer your questions as best as I can.
first of all I assume you have a 790cc engine, because I think the 865 engine uses a different setup for the crankcase breather.
1. The bonneville crank breather pipe - why doesn't the Speedmaster/ America have this? .
the answer to this is the america/speedmaster do have this pipe, on your pictures, the cover on the right is missing the breather pipe.if you have just taken the cover off of your bike it may still be attached to your bike, have a look.it passes back through the crankcases above the clutch and is connected to the black rubber hose that goes to the air filter housing.
2. The clutch mechanism cover that fits the standard bonneville cover - see mount holes - again why doesn't our bikes have this? will it be a problem if I don't install one?
not sure that I fully understand this question, but I think
the answer to this is, the cover on my america is the same as the pic on the right so I assume we dont need this part.
3. The cover inside the America cover near crank - what does it do? Is it only for oil flow which I presume is not needed if I swap covers?
this plate houses the crank end of the breather pipe and is only used on the america/speedmaster, if you look closely you will see that the breather pipe on the bonnie cover is already in its housing, so no plate needed.
I hope I have helped answer your questions, feel free to ask if you need more info, please let us all know how you get on with this as I am sure there are more of us considering this mod
good luck . steve.