Very tough question, but I'll give it a shot. This is more of a stream of consciousness than an answer, apologies in advance.
If I understand this correctly, you're given 2 equal sized sequences of strings, A and B, indexed from 1..n, say. You then have to find a sequence of indices such that the concatenation of strings A(1)..A(m) equals the concatenation of strings B(1)..B(m) where m is the length of the sequence of indices.
The first thing I would observe is that there could be an infinite number of solutions. For example, given:
A { "x", "xx" }
B { "xx", "x" }
Possible solutions are:
{ 1, 2 }
{ 2, 1 }
{ 1, 2, 1, 2 }
{ 1, 2, 2, 1 }
{ 2, 1, 1, 2 }
{ 2, 1, 2, 1 }
{ 1, 2, 1, 2, 1, 2}
...
So how would you know when to stop? As soon as you had one solution? As soon as one of the solutions is a superset of another solution?
One place you could start would be by taking all the strings of minimum common length from both sets (in my example above, you would take the "x" from both, and searching for 2 equal strings that share a common index. You can then repeat this for strings of the next size up. For example, if the first set has 3 strings of length 1, 2 and 3 respectively, and the second set has strings of length 1, 3 and 3 respectively, you would take the strings of length 3. You would do this until you have no more strings. If you find any, then you have a solution to the problem.
It then gets harder when you have to start combining several strings as in my example above. The naive, brute force approach would be to start permuting all strings from both sets that, when concatenated, result in strings of the same length, then compare them. So in the below example:
A { "ga", "bag", "ac", "a" }
B { "ba", "g", "ag", "gac" }
You would start with sequences of length 2:
A { "ga", "ac" }, B { "ba", "ag" } (indices 1, 3)
A { "bag", "a" }, B { "g", "gac" } (indices 2, 4)
Comparing these gives "gaac" vs "baag" and "baga" vs "ggac", neither of which are equal, so there are no solutions there. Next, we would go for sequences of length 3:
A { "ga", "bag", "a" }, B { "ba", "g", "gac" } (indices 1, 2, 4)
A { "bag", "ac", "a" }, B { "g", "ag", "gac" } (indices 2, 3, 4)
Again, no solutions, so then we end up with sequences of size 4, of which we have no solutions.
Now it gets even trickier, as we have to start thinking about perhaps repeating some indices, and now my brain is melting.
I'm thinking looking for common subsequences in the strings might be helpful, and then using the remaining parts in the strings that were not matched. But I don't quite know how.