Yes, an "Alternate transcript" would be a great idea for someone like yourself with a low GPA. Generally classes that you should consider are quant based classes or business based classes. These would include Calculus, Stats, Accounting, Econ. Also, remember that classes take a VERY long time, especially if you are working. So also, check out the 5th questions down on the UCLA FAQ (for EMBA's) here:
https://www.anderson.ucla.edu/x459.xml It talkes about a few options to brush up on quant skills. They have a class specifically geared towards business quant, and it's at UCLA extension. Might be a perfect place to start. BUT MAKE SURE TO GET A's. PS, your masters GPA will help, and make sure that if you go ahead with applying to an MBA you will have to create a story as to why you've chosen an MBA now that you already have a professional masters degree.
Good luck!