Running:

- I get messages like 'Error in usb_interrupt_write()' or
  'Error in usb_interrupt_read()' when running nftytool. What is wrong?

You probably don't have read/write access to the infinity device. Set
the correct permissions or become superuser to be able to use the
programmer.

- Something about libusb missing stops me from installing. What's
  wrong?
  
You need to install a newer version of libusb to make nftytool happy. 
For gentoo use: 'emerge libusb' or something similar. 
For slackware/others: sources are available at 
http://libusb.sourceforge.net/
As of this writing, 0.1.10a is the latest version of libusb.

- How do I activate phoenix mode on my programmer?

Something like this ought to do the trick:
'nftytool -p phoenix -- -p phoenix -f 3.58 -e'
