Although a Mojo 40 is a "40" size plane, it really needs a bigger engine than a 40 to perform well.
Not sure which 46 you have, but if it's a good running and good throttling engine, it will work OK with a 12x4 prop. Replacing the stock muffler with a MCP (mousse can pipe) will make it work even better on the Mojo 40.
But the best engine for a Mojo 40 is an OS 55AX. Replacing the 55AX stock muffler with a CCP (coke can pipe) turns it into the ultimate engine for "40" size 3D machines. No other glow engine really comes close.
Want proof? Here's an old video of my Mojo 40 with an OS 55AX and a CCP.
http://www.youtube.com/watch?v=gCda-xLW-Pw