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Okay, This info is from my own personal experience, and I find to be very accurate based on that. Details here are VERY IMPORTANT to know when programming the PCM, especially if the PCM is not from same vehicle as the engine. In some cases just a 1 year difference in parts will make the difference between a drive by wire system that works, and does not, and sometimes won't even throw any codes, simply won't work.
ENGINE FAMILY INFORMATION
Vortec 4.8 / 5.3 / 6.0 changes over the years: 1999-2002 mostly cable drive throttle. Computers used were 09354896 from 99-00, and 12200411 from 01-02. Both of these had red/blue computer connectors. Both the 99-02 PCM's will work with early DBW or DBC. Drive by wire throttle bodies 99-02 had two electrical connectors, one on each side (2 pin on passenger side, 6 pin on drivers side) I have seen drive by wire in some SUV's in 2000-2002 5.3 and 6.0 applications. 2003 ALL Pickup trucks and SUV's switched to Drive By Wire throttle, and the throttle body changed to a single 8 pin connector on passenger side. The computers used 2003 - 2007 had green/blue connectors. Express van's started getting the Vortec Gen 3 family of engines in 2003, and stayed with CABLE throttle through 2006. See below list of computers from 2003 to 2007 by Service. No. located on white sticker on PCM.
2003: Serv. No's: 12576106 *. 12581565 *. 12582605, 89017733 * (GM REMAN number for 12576106 * )
2004: Serv. No's: 12586242, 12586243 *
2005-2007: Serv. No's 12589462 *. 12589463, 12602801 *. 12602802 (Seems the 1258946x were mostly used in 2005, the 1260280x I have seen in a few 2005, and most 2006, and all 2007). I have also seen Serv. No. 28042802 in a 2006 5.3L application,
* = will accept cable throttle calibration (has chips in computer to control idle air controller valve) see here for more info on that
ENGINE SIZE SPECIFIC INFO
Vortec 4.8 / 5.3 differences: GM used a shorter stroke crankshaft in the 4.8L and a longer connecting rod. 99 to 03 or so, the 4.8L's all had completely flat top pistons. 5.3L's had a slight dish. However, after about 2004 sometime, the 5.3L's could have true flattop's. So really the BEST way to tell is measure stroke, or casting number on crankshaft. Of course if you are standing in-front of a vehicle, you can look at the VIN#. 8th digit is the Engine, 10th digit is the year. T = 5.3L LM7, V= 4.8L LR4, Z = 5.3L L59 Flex Fuel (1999 to 2007) Typically 1999 to 2002 were cable driven throttle bodies, however, some did get drive by wire as early as 2000 I have seen.
1999-01 4.8/5.3 Had EGR, 2002+ did not have EGR. 2002 most used a factory block-off in the intake. After 2003, all intakes should be cast shut in the EGR tube area.
2001+ Used MLS (multi layer steel) head gaskets. This can be identified by looking for a small brass rivet in the head gasket at each end of cylinder head where head meets block. Rivet = MLS
Vortec 6.0L differences: 1999 to 2000 6.0L's were all iron headed. Also the crankshaft flange extends out away from the rear engine cover by an inch or so. These two year 6.0L's WILL NOT bolt up to 4L60E transmissions from 99+ Trucks due to lengh
of crankshaft flange. Starting in 2001, all 6.0L's switched to aluminum heads with the '317' casting in the corner. Also the crankshaft flange is now almost flush with the rear engine cover. 2001+ 6.0L's that were mated to 4L80E's will have FLAT flex plate and will have a spacer between flex plate and crankshaft. The LQ9 6.0L was now also available in high end vehicles such as the Silverado SS, Caddy Escalade. The LQ9 sported flat top pistons to raise compression, and the LQ4 had slight dish. Both engines used the same 317 casting. You can also look at VIN number, 8th digit U = LQ4, N = LQ9.
2001 - 2002 6.0L's mated to 4L60E will all be drive by wire, using a throttle body with two electrical connectors, using red / blue colored PCM connectors.
FUEL SYSTEM INFORMATION
1999-2003 4.8, 5.3, 6.0 all had a fuel rail with 3/8" supply line and a 5/16" return line. The fuel pressure regulator is on the fuel rail, and has a vacuum line to the intake manifold. In 2004, truck engines went to a single 3/8" supply line, with NO RETURN LINE (returnless) except 5.3L L59 Flex Fuel vehicles. For 2004, Flex fuel engines KEPT the return line, BUT used a fuel pressure regulator with a lower pressure ratting. 2005 5.3L L59 Flex Fuel engines switched to a single 3/8" supply with NO RETURN line in 2005. Non flex fuel engines, fuel pressure spec is 55 to 62 psi with vacuum line disconnected, fuel pump running. 5.3L Flex Fuel engine 2001-2004, 48-54 psi with vacuum line disconnected, fuel pump running. 2005+ with returnless fuel rail all shared same fuel pressure spec, 55-62 psi. There is no vacuum reference on these, so fuel pressure should remain constant under all operating conditions. The computer is programmed differently for fuel flow rate depending on type of fuel rail. This is important to know when having a PCM programmed. (exception: 04 express van and 04 trailblazer/envoy still used return style fuel rail, 05+ single line, retunless rail)
Fuel injector flow rate is very important to have programmed correctly in your PCM. Find a small 8 digit number located on side of each fuel injector. Here is the breakdown.
25317669, 25320287 - 1999, 4.8L and 5.3L - flows 2.742 gm/sec or 21.8 lb/hr @ 58 psi
25317670, 25320288, 25323974 - 1999-2000 6.0L, 2000 4.8L and 5.3L - flows 3.125 gm/sec or 24.8lb/hr @ 58 psi
25317628 2001-2007 - 4.8L, 5.3L, 6.0L - flows 3.180 gm/sec or 25.2lb/hr @ 58 psi
25326903 - 5.3L L59 Vin Z, flex fuel 5.3L - flows 4.164 gm/sec or 33lb/hr @ 50 psi These are taller then the non-flex fuel injector *this injector only used on return style fuel rail, 01-04
12580426 - 5.3L L59 Vin Z, flex fuel 5.3L - flows 4.617 gm/sec These are taller then the non-flex fuel injector * this injector only used on returnless fuel rail, 05 to 07
12554271 - 1997-1998 5.7L LS1 - flows 3.727 gm/sec or 29.6lb/hr @ 58 psi
12555894 - 1999-2000 5.7L LS1 - flows 3.438 gm/sec or 27.3lb/hr @ 58 psi
12561462 - 2001-2004 5.7L LS1, LS6 - flows 3.781 gm/sec or 30lb/hr @ 58 psi
12613412, 12609749 - used in 2010+ Flex Fuel engines, these are drop in high flow injectors, that fit the rails on the 4.8/5.3/6.0 non flex fuel engines. (same injector height). These are 50lb/hr injectors. Good performance injector, and CHEAP on eBay. These do use the EV6 connector, like the L59 injector.