Stretch and Pitch not processing the entire clip

I did a quick sum. Assuming that this is mono, your file size is about 2.419 Gbytes, and every time you carry out an operation on the entire file, this ends up being approximately the length of the file dumped in your temp directory for the purpose of undos. I don't know what else, if anything, you've carried out in the way of processing, but if you allow just five undo, that means your temp directory has 12 Gbytes of data in it. Unless you are processing it as a 32-bit file, in which case you can double the numbers....  Now, I don't know how much space is actually available in your temp directory, but there's a not unreasonable chance you've run out of space, and it's just truncated the operation.

One thing you can try is to get an external usb drive of a reasonable size, attach it to your computer and re-assign Audition's temp directory to it (you can do this in Edit>Preferences). If it's big enough and with nothing else on it - which may not be the case at all with your existing temp - then I think you stand a rather better chance of success. How big? Allow several hundred Gbytes.