Look in FTPDataChannel.c. I believe most of what you need to modify can be found there. In particular look for the On* event callbacks after the transfer is complete. You should have access to all the details about the transfer around there including what byte range was sent/received, quota charged, etc. It should be easy to add an extra field to the On* callbacks to pass the bytes transferred and then you can track these in TCL manually using an ioVar to keep state.
Alternatively you could add a new variable in the FTP_VARIABLES structure included by the FTP_USER structure which is used to store per-connection information and is probably the only safe structure to modify as it has no other uses. The tricky part will be how you want to get access to that total as the cookie logic is really messed up, so adding a TCL function might be the easiest way since you don't care about EXEC scripts...
I'll probably add something similar to the next release for you so if the need isn't urgent just wait a bit
disclaimer: I didn't design this thing, I'm just maintaining it...
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