I know Cyrk ended up having to go with a custom fuel management. I would fire him a PM and see what he did. Sounds similar.
Though it sounds peculiar that a wiggle of the wiring brought about a CEL. That at least sounds easy enough to remedy with some splicing. God knows, the re-wiring during S/C install was a tedious POS.
I get engine studder occasionally in my VX, but it's only when I have it running, turn it off long enough to run into a store or something, and then start it back up. Only happens on restart. I rev it up to about 2k rpms for about 20 secs and it purrs on its own again. I am sure that is fuel related. I still have yet to replace my fuel filter so it may have somehting to do with it (I am hoping).
Good luck.
Gary Noonan
'01 S/C VX / '18 Forester XT