Acceleration/Deceleration was a tricky one to get working as there is very little processing power left to do it. The way it is currently done is a little bit of a hack, but it should be possible to slow it down.
There is one calculation you need to change. On Lin 656 (I think) you should find the following:
cmd.stepRepeat[motor] = (byte)((18750+(divisior>>1))/divisior)-1; //note that we are rounding to neareast so we add half the divisor.
If you increase 18750, it should slow down the acceleration/deceleration curves. Trouble it, it's not a straight forward relationship. If you double the number for example, it will roughly but not quite double the length of the acceleration time. If you want to make that number larger than 65000, make sure you add 'UL' as a suffix (e.g. 75000UL). In practice you shouldn't need to go that large. Maybe try something like 30000, see where it gets you.
Part of the issue is that there is a 1/x relationship in the speed, so at higher speeds it takes smaller increments to keep going at the same rate. Calculating 1/x is quite tricky especially as once you get to about 20x speed, all of the values are <1 which means it starts accelerating very rapidly (not what we want).
