I will try my best to answer your questions.
I use flashfxp. A great program, use it to FTP to my xbox 1 as well. Though it is shareware......
Secondly, I set flashfxp to "Active Mode". This was accomplished by going to (in flashfxp) Options > Preferences >Proxy. Here you will see a check box beside "Use Passive Mode" be sure this box is UNchecked.
Since you've already disabled xbox live access from the console itself, you should be ready (at least that is what I've done thus far).
When you wish to FTP to your xbox 360, start xexmenu on your console, then simply click "Quick Connect" (in flashfxp), then enter the IP address of your xbox 360 in the "Server/Url" fiield (the IP address can be obtained from xexmenu). The user name will be "xbox" (no quotes), and the password is also "xbox" (again with no quotes). Then click connect and it should connect

Why exactly do you need to uncheck the "Use Passive Mode"......just wondering what this does when it is checked versus when it is not checked.
I have transferred XBOX LIVE GAMES, Emulators and Apps and they all workd perfectly.
One more question though. I am using a OEM 120 GB XBox 360 HDD and there seems to be a problem with transfering a certain amount of SNES ROMS......is there a limit to the number that can be in a folder. I have about 11,000 SNES Roms.... any advice.