I often put a waypoint at start and end of motorway sections, then just add them up to get an idea of motorway miles, years of trips has given me data, and expereince, so I know UK Motorways 60mph average is often ahrd to achieve, but France it is fairly eays to manage 65+ (setting cruise to genuine 81mph speed limit)
Main roads in Europe is around 50mph if I am not too anal about the 80KPH "limit" on deserted D roads, hard to get much more without going ape shit as you still have towns and villages, N roads can be a bit higher, but baiscally I assume 65 for Motorways and 50 for N/D roads is it is pretty close.
In good dry conditions we typically beat the times given by MRA - I use Google, Here and Tom Tom calculation engines and assume if good weather, no roadworks, diversions or getting lost that we will beat them, but larger groups, bad weather or bad luck can add delays so I leave a bit of wiggle room.
For each hours ride I assume a 15 minute fuel / piss / coffee stop will be required, and add an extra 30 mins for the lunch stop - so a 5 hour ride (250 miles back roads) will include about 2 hours of stops = 7 hour day, Mountains are much slower, in the alps / pyrenees averages come down to 30-35mph riding pass after pass, so I only plan for 150-180 miles, and you tend to stop more.
I also try to plan for things changing, I may split a route into two halves (AM / PM) and then do a second version of each in case of bad weather or delays, so you have 4 possibilities, so if it is pissing down in the morning I may take the easier AM route, or if it starts pissing down at lunch time take the easier PM route. Worst case just pump the Hotel address in to the nav and lat it take you the fastest way there - no point teetering about on wet muddy back roads in pissing rain IMHO.