Intercept the condensed methanol in a liquid trap. Take great care because methanol is highly flammable and the fumes are explosive. This is basically the same as heat extraction, but it requires less energy. The drawback of this method is that you need a special vessel and equipment to do this. Build the reactor, get confident with the process and eventually upgrade to methanol recovery.
Diesel engines require fuel of a certain quality.
You just can't pour poor-quality biodiesel into the tank and expect the engine to go on and on without problems. A proper wash will get rid of the glycerine and neutralize the remaining lye. There are also kits available for various quality tests. I was told in a letter from one of the visitors to our site of a test used by the motor industry for determination of glycol in motor oil. This should work for free glycerine determination.