You should only need $qt() around the path/filename. For mIRC to know that your path/filename has spaces in it and that it's not a new piece of information (aka parameter) for the command, quotes need to be used. That's what $qt() does. The parameters should not need quotes.
The only limit you should see on a command like //run is the Windows maximum path length, which used to be 256 characters, but I am pretty sure it's been bumped up a lot since XP. Most other commands have around a 4000 character limit in mIRC.
If it is cutting something off, then there may be some error in your script. If you show the full script that you are using for the part that is getting cut off, someone can tell you where the problem is.