Unfortunately, the cold start map for stock injectors doesn't suit larger injectors well, which I think is part of the issue you're seeing.
Do you have your O2 sensor hooked up, and is it starting to function properly by the time you see the RPMs start dipping?
I'm almost positive this is an AFR related issue, and the roughness you're feeling are lean misfires.
You wouldn't happen to have a wideband or access to one for this would you? It's the most important gauge IMO, and I think it'd tell you a lot about what the ECU is doing.
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