Is there a difference in aerodynamic efficiency between single engine and twin engine airplanes?
Your question really needs further bounding to be able to accurately answer.  I will discuss a few aspects.

First @ratchet freak is right on the money.  What engine mount are we talking about? A podded engine on the single and twin (or multi, since your one of your questions mentions multi) or some different configuration.

In the late 70's and early 80's there were a bunch of academic and not so academic papers and articles written on the topic.  Generally the focus was on the Cessna 336/337, O-2 and Defiant type aircraft.  There were also papers on a loss of engine scenario.  This got rekindled for the Voyager aircraft design and promotion.  The Voyager had a L/D of 27. And it was intended that one engine shut down in cruise flight.

The 61 knot rule for single engine is said to be influenced by crash survivability. I get that, but I will editorialize that several studies have shown that the chance of something bad happening with the loss of an engine is greater in a multi. 

Top speeds, stall speeds and mass (weight) are different parameters, subject to different trades.  Furthermore, putting this into the context of existing, production or some arbitrary subset of the universe makes your question hard to answer.

The real answer is that one can design for what you need.  You can have a very slow stall speed in a single or a multi, what would you like?  You can have a nice L/D with any number of engines, what would you like?  And you can haul lots of stuff, although there are not heavy singles around. But to generalize all three parameters, of these non-linear trades, into one rubric, would likely challenge even the most mathamatically talented aerodynamcists that I know.  If you can tighten the bounds on the problem, you might get a better answer.