The term GP38-3 is really unofficial and the work done to the locomotives varied a lot, depending on the rebuilder. Generally, the engines were GP38-2's with upgraded electrical wiring and modern solid state controls. There were no external changes made. Other GP38-3's have used everything from GP-35's to GP-50's. Some had engines derated to 2,000 horsepower, with turbochargers removed, and were extensively rebuilt, with new cabs, air conditioning, and larger fuel tanks. You really need to know exactly which road's GP-38-3's you're asking about since there was a wide range of changes made. GP-40's were rarely used as the basis for a GP38-3, however.
There's information about the SD40-e's, which were rebuilds from SD-50's, at
http://www.altoonaworks.info/rebuilds/ns_sd40e.html. The CSX GP50-2's were just standard GP-50's derated to 3000 horsepower with no external changes. They are used mostly in MOW service. The GP40-3 is also a generic term for locomotives rebuilt by several companies, including Helms Leasing and Conrail's Juniata shops. Most were simply original GP-40's, derated to 2,000 horsepower with the removal of the turbocharger, with some upgrading to the wiring and control systems. Some also got upgraded cabs, with air conditioners and new control stands. They were not upgraded to GP40-2 standards internally. Most had few, if any external changes.