The green wire at the coil is what tels it to fire, I think, If you have power on the red and green wires, your prob. lies within the tfi mod or the wiring to it.
I had the exact same prob with my 2.9. I replaced everything also and still no luck. I noticed that when I jiggled the wires around going to the tfi mod, the ignition relay would click on and off showing that I had a ground out wire in that section of wiring. After fooling with this prob for about 2 weeks, I went to a Junk yard and got the harness that goes from the tfi mod to a gray plug sitting on the pass. side valve cover(It has 7 wires i think and its maybe 8 inches long). this fixed my prob and it started right up. I had a wire that was grounding out inside of the tfi ignition shield, a black covering that goes over 3 or 4 wires on that harness. That is something you may want to check
Also, there are two black wires, like 10 ga. I believe, that are coming from your battery, which i believe is a ground for your comp. Mine were all corroded making me have no spark after I had fixed the prob
Hope this helped