If your coil resistance is 5.5 ohm and the rated current is 2 A, then the rated voltage is probably 12 V, not 24 V. With the current limit set to 350mA, a pair of 5.5 ohm coils should only need about 2V to be driven, so using a lower power supply voltage would be the most straightforward way to help your problem, but the A4988 only works down to 8V.
This thread on our forum discusses a similar problem and might be helpful for you. Using a different driver that offers a full-time fast-decay mode might help you get a smoother motion. Our new DRV8880 carrier board has an AutoTune feature that automatically selects the decay mode every PWM cycle in an attempt to optimize current regulation, and it can be placed into full-time fast-decay mode (or one of eight other decay mode configurations) if that does not work.
Also, this blog post discusses using diodes in series with the stepper motor to raise the threshold voltage at which current flows, which seems to have worked OK for them and seemed to help when I did some testing here.
-Nathan