There were differences such as most, if not, all DOHCs that came in Neons had combined intake air temp. and MAP sensors where the DOHC used in the Eclipse had seperate sensors to do each function. This is why the Missing Link for the 420A cannot be used on a Neon DOHC engine.

Ignition timing with a stock ECU isn't really a problem either as it works pretty well to a point even with a turbocharger.

I'd be more inclined to believe its a fuel issue as stated. Either your injectors are too small or sticking or your rate of gain is not high enough and your leaning out.

Other then melting plugs or knowing how to read them, I'd like to know how you came to the conclusion it was detonation. What do the AFRs look like in boost? Are you going above 13:1 at any point in time? Without a wideband or something to monitor the AFR, there isn't much a untrained eye or ear is gonna pick up.