2011 e70 35d misfire, smooth running, inection monitoring after replacing GPs & GPR

[hellspcangel911]

Hi all,
You know that overwhelming feeling of disappointment when you finish the repair, start the engine and the CEL remains......hoping you guys can help me figure this out.
Car has 120k on it, it ran well but had a code for #2 glow plug and occasionally the relay. I pulled the intake, found moderate carbon build up cleaned that of, replaced all of the glow plugs, the glow plug relay, removed and plugged the swirl flaps and replaced some of the vac lines located under the intake with silicone hoses.
Cleaned everything up, new gaskets, new air filter, cleared the codes and started it up. It ran a little rough but hoped that would go away.
After a few attempts I still get rough idle at start and at temp, significant vibration/shuttering from the front right around 1800-2100 rpms and the following codes
p0270- Cylinder 4 Injector Circuit Low

4592 Smooth running Controller, Cylinder 4
4CE8 DDE MISFIRE DETECTION CYLINDER 4
459C SMOOTH RUNNING CONTROLLER CYLINDER 1
4679 FUEL INJECTION RATE MONITORING
4929 DDE INECTOR CYLINDER 4 ACTIVATION

P1729 HIGH IRREGULAR ROTATION
4F6F HIGH IRREGULAR ROTATION

So its obvious I messed something up but I'm not sure what, I was pretty meticulous when I completed this. The car is stock, I removed the swirl flaps with the intention of doing a full DEF/SCR/EGR delete in the Fall.
Before I pull the intake and check everything, any suggestions what to start with?

Thanks