Here is are 2 dumb question:
1. Since enhanced ctorrent seems to be command line compatible with the asus ctorrent program, why not just replace the ctorrent executable in the custom firmware with your enhanced ctorrent version? That way the asus utilites should work together with the improved torrent client?

2. OR install enhanced ctorrent to the opt directory and change the name to ctorrent. That way if the system finds this ctorrent before the built in asus version it will use the fixed version without the file size limitation?