Yes, capacitance does make a difference. First, it can't be too small. Because the caps is there to remove any DC input just before the opamp, they form a high pass filter together. When the capacitance is too small, you will start to lose most of the sub-bass. The stock Wima is 2.2uF, which is a fairly safe number to use. I'll suggest you should at least match it, if not higher. Too high a capacitance also won't help, so keep it reasonable, probably around 10uF~22uF, which will give you some good selection of caps that can still fit inside E12DIY without problem.
So I guess it would be OK to order electrolytic caps that match the values of the Elna Tonerex that came with the E12DIY as an alternative?
If I remember correctly, they are 10uF/25v.