One thing you could do is lay out some strings on the jig you have. Once you cut them off the jig measure them to see how much longer they are than the length the jig is set for. That difference is what you want to add for your short strings.
For example: If I set my jig to 50" and then find that the cut pieces are 66", then I want to add 16" to the finished length for the short strings I'm making. If I need a 40" string, I'll cut the strands to 56" (40 + 16= 56).
Jigs make the measurements convenient, especially if you make a number of different lengths. But you really don't need a jig, you just need some way to measure the strands.
Guy