Well, I uninstalled SH4, deleted my saves, reinstalled everything in the proper order (SH4, Uboat Missions, RFB, RFB patch, RSRD, RSRD patch) using JSGME, and started a new (third) campaign. First patrol, I encountered a taskforce of 10 destroyers, attempted to engage, got my periscope spotted, and got thoroughly depth charged!
Two things were different this install- one, I used JSGME rather than manually installing mods, and two, I installed RSRD (before I was using RFB alone). So, don't really know what fixed my problem, I'm just glad the IJN is finally on the job!