Don't mean to crap on - just brainstorming a little on the topic.
The reason they are different may be, firstly, physical factors such as weight, fuselage dimensions, drag coefficient, engine type and thrust, sweep angle of the wings (you will notice the B747 has a much sharper sweep than the A340 for instance), etc...
Then there are the financial connotations. Calculating cost per seat/mile is reliant on the configuration of the aircraft (how many seats in each class / how many seats in total). Then there is the optimum distance that these aircraft have to operate before efficiencies are gained. Oh, and don't forget cargo capacity as well, as this contributes a lot of revenue, particularly on long-haul international service.
I don't by any means want to discourage you, more encourage you to narrow your focus on what it is you want to achieve. It may be a straight-out comparison of operating costs at fixed configurations for each aircraft. If this is the case, you may want to create a sensitivity analysis, which looks at both aircraft types over a series of distances to work out which one is the best for certain markets (eg. over 1000nm, 2000nm, etc...).
If you can figure the lot out, maybe you should look at a career in Fleet Planning?