Do you see a difference in performance when running a standalone game versus editor, or only in cooked builds? Running with -game is a lot easier to test and iterate on than cooked builds and should be pretty similar.
Have you done any profiling yet? Use Stat scenerendering to compare same scene when it is fast versus when it is slow. If number of draw calls is dramatically different, you may have things instanced or loaded multiple times somehow.
Stat dumphitches will write a stat capture of all events above a certain threshold to log whenever you hit a slow frame. is first go-to tool for tracking down hitches, and should tell you exactly what your once per second hitches are doing.