I ran the engine with the valve cover off to verify valvetrain movement was correct. Compression test showed great compression across the board. Pulled the fuel rails and the fuel pressure regulator had disintegrated stopping up the number two injector. I went ahead and replaced all the injectors when I replaced the regulator. The engine is running great with rebuilt heads and new bolts and gaskets everywhere.
Still have the limp mode problem, reading all the information I can find about it, have started diagnosing the problem, but haven’t found it yet. I have the wiring diagram.