Mr. Mhan:
It appears you have a wheel that has a built in coaster. Meaning that bearing locks in one direction and freewheels in opposite direction. Is this correct?
If so, it was probably designed to run with a jack shaft. A jack shaft transfers power to other side of frame which would correct your assumed problem.
Adding a jack shaft will make things more complex. Supports and bearings will have to be added which translates into more dollars, work, time, effort, and unnecessary weight.
Try to avoid this if possible. Try to get a wheel/sprocket assembly that does not freewheel or figure out a way to lockup the existing wheel/sprocket assembly.
To flip over engine and then reverse it's direction of rotation would not be cost effective. Would likely cost many times what you paid for engine to begin with.