Did you download mkfifo from the GNU site? Can you drive it from the Windows command-line?

I suggest you take a look at the Avis::TreeTagger module code - it does nothing more than run the TreeTagger program attached to named pipes. I would not use it on Windows because it uses UNIX hard-coded path names and fork/exec.

In theory all you have to do is run the TreeTagger program only use IPC::Open2 instead. You will then have two file handles to anonymous pipes instead of named pipes.