How does the battery voltage look? I see you had inj4 issue and now misfire in cyl2 and the inj4 fault was an actual electrical issue not a poor/incorrect flow issue..
obd2/vcds logging values for battery should be pretty accurate. sounds like you're running an aux charger while the car is running? no idea how that would affect things.
odds are the misfire is just injectors, maybe the TSB for the vw fuel additive is relevant, but I've never had much luck with additives.
pretty much any aftermarket intercooler would be a decent upgrade, if you're going to be near the NC area hit up jake @ baun performance for one of his.