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Hello, unplugging the GPCM shouldn't have affected any of these items. Unless the fan was unplugged or the VGT solenoid. The cold start I would suspect you have a faulty GPCM as they are known to go back and cause a hard start.
If you aren't building boost and have a deeper noise under the hood. I would suspect the CAC hose has come off the turbo or cooler. That can also cause the P0046 and no turbo boost.
The best way to test the GPCM is to unplug one of the glow plugs and test for 12v here. When you turn the key on it should easily hold battery voltage. If you are only getting 9 or 10v then the glow plugs aren't getting enough voltage to get hot enough.
The solenoid might have some carbon build up. I remove them and clean the Oliver off the end with some very fine sand paper and this should help.