There is a nice and short description how to "merge" a Proto shell and a Trainman drive.
http://www.iaisrailfans.org/gallery/GP38-2-repowering
It reads quite simple and it is really as simple as it appears.

IMG_5156 by faraway52, on Flickr
IMG_5155 by faraway52, on Flickr

I used the model as a testbed of the new Tsunami2 PNP EMD sound decoder. It worked just fine and the slow speed could be set with the 28 step curve without any hassle. Decoder Pro (JMRI 4.4) missed the important prime mover selection CV 123. A new decoder file must be installed. That process is nicely explained here
http://www.dccguy.com/?p=1302

The plan is to have some lightly modified Trainman drives with sound decoders to be base for many Proto 2000 GP38-2 shells. Swapping the shell is quite easy. I have a bunch of old CSX, CR , NS, CP and BN Proto GP38-2 models/shells benefiting from a Trainman drive with sound decoder.

ps. It is basically the same technique as I use it with heavy modified Trainman drives to support multiple Athearn Genesis GP38/40-2 shells.