Terrific!

I am confused though, if your Mac Plus is the server connected directly to the Internet, what does the Quadra and Linux box have to do with anything?

Also, why transfer your files from the 128K using Xmodem on the Plus? Why not use MacTerminal on both? I use MacTerminal to transfer files between my OSX Mac and 128K all the time and the files are perfectly preserved, and function correctly in Mini vMac. Http://mac128.com/transfer

You might try keeping everything native Macintosh for your file transfers and see if that solves your problem.