I've been advised that an APR fuel pump is essential with stage 2. I'm going to be buying the stage 2 package from JKM as soon as I have the cash to do it all at once. Too many compromises to do it parts, and stage 1 is working very well at the moment. I wanted the APR RSC exhaust on first for the sound but the lack of back pressure would mean adjustments being made in lieu of the other hardware not being fitted to prevent erroneous errors.
If you don't have an uprated pump I would guess that, as a non expert, that fueling is at the root of this. Have a look at JKM's package and see what you don't have that they include and see if it has any relevance. They're package is well researched and proven.
Good luck!