** Note: It is best to use a transmission from a 97-02 as changes made in 03+ models may require additional work.
Information sourced from: http://www.tripleedgeperformance.com...bout_using.php

There are a number of changes in the 2003/2004 and newer 4T65E transmissions, and below is a simple list of the main differences.

1. Beginning around June of 2002, which will apply to 2003 model years, the valve body and oil pump assembly were changed. Changes are rarely made because it is better or needed, but rather than to simplify assemble and lower costs. Some of the new style pumps were fitted to the old style valve body, while some of the old style pumps were fitted to the new style valve body. The older style being a 2 piece pump and the new style being a 3 piece pump. These will NOT interchange without a matching valve body!

2. The Valve Body changes are minor, though must be used with the appropriate oil pump and Fluid Pressure Switch Assembly. Most all 2003 model year vehicles received a newer style valve body which incorporates a much smaller fluid pressure switch as it only detects TCC operation being ON or OFF. The older style fluid pressure switch assembly had a total of six pressure switches which would detect fluid pressure present during each gear currently applied and signaled the PCM this information. This change alone is a main reason the 2003/2004 and up transmissions WON’T just readily work with an older car as the PCM is different and no longer uses the fluid pressure switch on the newer models.

3. The Pressure Control Solenoid, PCS is different and will NOT interchange, though it may physically fit in either valve body. The solenoid is designed different and does not function the same as the earlier units. If used it can destroy a good trans because pressures will not be correct as the valve body is calibrated different to be used with the new style solenoid as well as different PCM calibrations were made.

4. The Internal Wire Harness was also changed to work with the above changes, as well as most all models used an Internal Mode Switch, as the earlier models had one that bolted on the outside of the trans case located directly under the manual shift lever. Some 2000 and up models already incorporated this and it CAN be used in vehicles that came without it with minor modifications to the wiring harness OR by just bolting on an older style switch as it was on the original transmission.

5. 2004 and UP TapShift style transmissions use a UNIQUE valve body and channel plate and WONT work without the proper PCM! The manual valve linkage and manual valve inside the channel plate is different, as well as the separator plate and valve body to accommodate these changes. It simply put WONT work and should not be tried.

6. ALL channel plates from January 2004 and up included an internal converter drain-back ball and spring. Because of this, this channel plate is not interchangeable with earlier models. From what I have found most 97-99 transmissions also used this with an earlier style Thread-In cooler line fitting. From 2000 and up they replaced this type of fitting with a quick connect fitting and these had a drain-back ball and spring in the return cooler line fitting, while the 97-99 transmissions did not. While it is certainly possibly to use the 2004+, or 2006 transmission for that matter the channel plate and valve body must be replaced BUT you must check to make sure the original channel plate also had the drain-back ball and spring. The return cooler fitting in the case was changed and was made a different thread size on purpose so you cannot use an earlier style fitting in the case as this would create a very bad restriction in cooler line flow.

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Disclaimer: All information provided in this article is for reference purposes and is believe to be correct by the author at the time the article was completed.