Just be sure and notate which ships came from FotRSU. You might also try to trace their lineage, since some of them in FotRSU are recent additions, and we only got permission from the authors for inclusion with FotRSU. There is a list of those vessels in the ReadMe stuff in the first posts of the FotRSU thread, as well as in several places of the Support folder in FotRSU. There are other ReadMe in folders below the Support folder that mention who built what, including the old FOTRS ReadMe files...
As for the AI Torpedoes, there is quite a lot of Library folder work and eqp file work you would have to do, and the "lineage" of that particular 'weapon' goes way back, and was edited by s7rikeback and CapnScurvy, also noted in the FotRSU thread as well as the ReadMe stuff in the mod. The sim file also controls them, since that controls the "Range" of functionality... I have no clue about those things, and if you give up on them, just delete their entries in the equipment file, and renumber as necessary. The nodes for them on the ship would do no harm being there.