I used the numbers from the Finnish state research centre VTT (http://lipasto.vtt.fi/yksikkopaastot/tavaraliikennee/vesilii...)

Looks like a useful table, but unless I've missed it you need to know how many people/cars are on each ship?

My understanding is that these numbers (try to) account for actual real world usage rates. Actual emissions will of course depend on a whole lot of things, including the things you mentioned, prevailing winds, etc. Same for estimating grid emissions for charging the car of course - the exact mix of sources is always in flux.