I've thought of doing this very thing before. You can not use a transformer on DC voltage. What you need is a DC-DC converter. (Sure, they use either a transformer or coil inside, but they have a bunch of other electronics to make the DC into AC, step it up and then turn it back into DC).
I think what you want is another battery somewhere. By the time you're done, you should have double the stock current to the window motor and that would require a big DC-DC converter. You might try a 2V Cyclon cell (or two) in series with your regular starting battery. These are quite good batteries with low ESR (you could probably use 6 of the large ones instead of an Optima). Or you could use a complete 14-16V gel cel. Then you just need a floating charger (i.e. DC-DC converter with isolated input-output) for the 2V or 4V cell and reroute the window circuit there. You might be able to use something as cheap as this:
http://www.ebay.com/itm/NEW-DC-DC-600W-Step-Up-12V-60V-to-12V-80V-Power-Apply-Module-High-Power-/331043297078?pt=LH_DefaultDomain_0&hash=item4d13b7d736
Since the windows run on switched ignition, having a large DC-DC converter would have the advantage of running the windows as much as you want with the engine running. With small batteries, you might run them down and you'd have to run the engine for a while before the windows work again. Duty cycle on windows is normally pretty small, so unless you deliver mail in the rain or something...
I don't think the extra voltage will hurt the motors. A circuit breaker is a good idea, though, in case a relay sticks or somebody keeps holding the button...
The other advantage to either of these setups is that the window speed is going to be almost constant whether the engine is on or not. A big adjustable DC-DC would be the best, as you could just "dial-in" the speed you think is best. But that could be an inefficient unit that draws a lot of current whenever the key is on.