I know it's kinda late to change what you've done, but there's a product available that gives you the perfect preslope and final slope to you shower without having to worry about whether you did it right or not. Here's the link. It also comes with an all-inclusive installation video.
I would suggest however that if you are having pooling on your membrane, then you will have pooling after you put in your final slope also. If water permeates through your tile and final mortar bed, then you will have pooling on your membrane that will create mold.
I don't see why you couldn't just remove the membrane and add to the pre-slope. If that won't work, you might have to start over and could use this kit and get perfect results for both your prelope and final mortar app.