Yes. It would actually be much better (and simpler) to have a single conditions file with three columns: one for the condition name, one for the prime, and one for the target.
All three variables will then automatically be linked together in the same row for each trial in the data output file, in a sensible columnar arrangement.
This also means that your Builder flow arrangement reverts to a simple single loop arrangement, rather than the current set-up of nested loops.
And this post will show you how to still have just a periodic rest routine even though you have just a single loop: