I had this problem last year. I was using 1 bag straight out the back. I went to 2 large(48") bags. One on each side. And used more throttle.
I do still get the speed jump on the GPS. I have the Elite 5 so it's a similar model. In choppy waters I do my best to average and take the speed it's closer to more of the time. With te new bag setup and less that 3 ft waves I can usually keep the speed from jumping more than .3mph.