There's a technical service bulletin that outlines your exact concern. Here's a copy of it and how to fix the problem:
Diesel Fuel System - SES Lamp On/Injector Driver DTC's
Bulletin No.: 06-06-04-026A
Date: December 08, 2006
LLY Intermittent SES/MIL Lamp Illuminated, Reduced Engine
Power, Fuel Injector Driver Circuit DTCs P0201, P0202, P0203, P0204, P0205, P0206, P0207, P0208 and Cylinder Bank Shut Down DTCs P2146 or P2149 (Replace Affected Injector Connector Pigtail Harness)
2004-2005 Chevrolet Kodiak C4500/C5500 Series, Silverado Models
2004-2005 GMC Sierra Models, TopKick C4500/C5500 Series
with 6.6L Duramax(TM) Diesel Engine (VIN 2 - RPO LLY)
This bulletin is being revised to update the Kent Moore tool number used on inspecting the injector connections. Please discard Corporate Bulletin Number 06-06-04-026 (Section 06 - Engine/Propulsion System).
Some customers may comment that the Service Engine Soon lamp is illuminated and/or intermittent along with a significant reduction in engine power (limp home mode). Upon investigation, the technician may find one or multiple injector driver circuit diagnostic trouble codes (DTCs) P0201, P0202, P0203, P0204, P0205, P0206, P0207, P0208 and bank shut down DTCs P2146 or P2149.
If the published diagnostics lead to an injector connector on cylinders 2 and 7, the 2 and 7 cylinder injector connectors must be repaired and supported as per bulletin 05-06-04-047B.
If the published diagnostics lead to an injector connector on cylinders 1, 3, 4, 5, 6 or 8, replace the affected injector connector pigtail harness with P/N 88988963 using the following repair procedure.
Complete normal SI diagnosis for the trouble codes set.
Injector circuit or injector coil tests may be normal until the engine reaches operating temperature. Recheck circuit/injector resistance readings with a warm engine.
Dealer technicians are to repair wire chafes at the Fuel Injection Control Module (FICM) as needed. Follow the correct SI wiring repair procedures. Insulate the harness from the aluminum retaining bracket with suitable material (electrical conduit or heater hose) so the harness will not chafe again.
When diagnostics are being completed for Injector Driver Fault codes, the dealer technician may notice the Fuel Injection Control Module (FICM) connector is wet or has a wet residue on it. The FICM connectors do have a type of dielectric grease that may be mistaken for diesel fuel. The FICM should not be replaced if this type of wet residue is found. Clean and dry the connectors as needed. No extra dielectric grease needs to be added to the FICM connectors.
Inspect for wire harness chafes on the Fuel Injection Control Module (FICM) wiring harness retaining bracket. This is an aluminum bracket very close to the FICM connectors. If any part of the taped portion of the harness is touching the FICM wiring harness retaining bracket, then you must look for chaffing on the wiring harness. It must be disconnected from the FICM and bent back towards the engine. Look for any chafes into the tape. If necessary peel the tape from the area and look for any chafes into the wires. Some of these chafes are very small, possibly the size of a pen tip, but could still cause injector circuit concerns.
If diagnosis is inconclusive, inspect the injector connections on all related cylinders. Pin drags and terminal tension can be checked with Kent Moore tool number J 35616-35.
Clear the trouble codes and then wiggle test the related injector connectors to see if the trouble codes can be induced. If the vehicle had only injector circuit codes for P0202 or P0207 (with bank shutdown P2146 or P2149), and the wiggle test induces a P0202 or P0207 to reset, use bulletin number 05-06-04-047B to repair the injector connectors and install the injector harness support kit.
If the trouble codes or customer concern is induced during the wiggle test on any other cylinders (other then P0202/P0207), replace the affected injector connector pigtail with P/N 88988963. This replacement pigtail can be used to repair any cylinder except number 2 and number 7. The 2 and 7 cylinder connectors must be repaired and supported as per bulletin 05-06-04-047B.
Let me know if you have any more questions!