Okay, well first off, to use MIDI with the Empress Phaser or Tremolo2, you're going to need the Empress Midibox: http://www.empresseffects.com/midibox.html
There's a bunch of different ways to generator MIDI clock signal. Any DAW worth it's salt (like Protools, Cubase, Nuendo, etc), will do it. You can use a program like MIDI-OX to do it. Or if you don't want to use a computer, there's a bunch of different options. Here's some:
Molten Voltage Tempode - $139 USD
Ploytec 34oneII - $175 USD
MIDI Solutions Footswitch Controller - $149 USD (this one is going to require some programming)
Shoot us an email at firstname.lastname@example.org if you need any help getting things going.