rough idle and stuttering on acceleration

I have a 2006 VW Jetta BRM motor with 174,000 miles and I just recently had the cam replaced with a BEW reprofiled cam, new timinge belt kit, a new single mass flywheel installed, and injector 4 replaced with a rebuilt injector. The hard start issue has disappeared, but the car is still idling rough at times and stuttering upon acceleration. I am leaning towards pulling the injectors and having them rebuilt. I am new to VCDS and need help interpreting all of the following information. Please let me know if there is more info I should include in the post. The torsion value is at 0.0 and the guy who did all of the work is a trusted TDI mechanic, but lives three hours away and I can pull and replace the injectors myself. Great site and thanks for the help.
The engine fault codes from VCDS are
Address 01: Engine Labels: 038-906-016-BEW.lbl
Control Module Part Number: 03G 906 016 AB HW: 028 101 223 8
Component and/or Version: R4 1,9L EDC G000SG 7550
Software Coding: 0050071
Work Shop Code: WSC 00066 000 00000
VCID: 63C56B22A215AE06F53
3 Faults Found:
000769 - Cylinder 1
P0301 - 000 - Misfire Detected - Intermittent
Freeze Frame:
Fault Status: 00110000
Fault Priority: 0
Fault Frequency: 32
Mileage: 275960 km
Time Indication: 0
Date: 2000.00.00
Time: 08:39:11
Freeze Frame:
RPM: 798 /min
Speed: 0.0 km/h
Load: 0.0 %
Voltage: 14.21 V
Inj. Quantity: -1.84 mg/str
Temperature: 73.8°C
(no units): 0.0
000768 - Random/Multiple Cylinder Misfire Detected
P0300 - 000 -
Freeze Frame:
Fault Status: 01110000
Fault Priority: 0
Fault Frequency: 9
Mileage: 276231 km
Time Indication: 0
Date: 2000.00.00
Time: 12:40:37
Freeze Frame:
RPM: 798 /min
Speed: 0.0 km/h
Load: 0.0 %
Voltage: 14.21 V
Bin. Bits: 00001011
Temperature: 74.7°C
Bin. Bits: 01010000
000771 - Cylinder 3
P0303 - 000 - Misfire Detected - Intermittent
Freeze Frame:
Fault Status: 00110000
Fault Priority: 0
Fault Frequency: 15
Mileage: 276592 km
Time Indication: 0
Date: 2000.00.00
Time: 16:49:28
Freeze Frame:
RPM: 798 /min
Speed: 0.0 km/h
Load: 0.0 %
Voltage: 14.21 V
Inj. Quantity: -1.13 mg/str
Temperature: 72.9°C
(no units): 0.0
Readiness: 0 2 0 0 0
Here are the injection deviation quantities during acceleration from VCDS.
17:28:10 Group 013: Idle Stabilization (Injection Quantity Deviation)
-1.60 mg/str Injection Quantity Deviation Cyl. 1
-0.16 mg/str Injection Quantity Deviation Cyl. 2
-0.71 mg/str Injection Quantity Deviation Cyl. 3
2.52 mg/str Injection Quantity Deviation Cyl. 4
Here are the injection deviation quantities at idle.
17:23:12 Group 013: Idle Stabilization (Injection Quantity Deviation)
-0.31 mg/str Injection Quantity Deviation Cyl. 1
-0.40 mg/str Injection Quantity Deviation Cyl. 2
-0.07 mg/str Injection Quantity Deviation Cyl. 3
0.80 mg/str Injection Quantity Deviation Cyl. 4

have you replaced the fuel filter?

Update

I forgot to mention that I have replaced the fuel filter and ran 1L of diesel purge through the injectors. Any help in diagnosing the problem would be much appreciated.
Thanks,
Chad