I just gently pry them loose with a flat tip screwdriver. This must be done carefully since the ends of the motor can be easily damaged. As for installing flywheels, superglue gel works wonders.
regular superglue may not be the best choice. It doesn't hold up well to torque. A-Line / Proto Power West sells special glue for flywheels that is cheap, and works. I used it when repowering my E60 dummies, and so far they have not broken yet.
you don't need a wheel puller to remove flywheels. Simply twist the fly wheels in opposite directions simultaneously. this will break the bond that the flywheel is glued with on the shaft. they should simply slide off with little effort.