After putting the 74LS74 onto the board and its failure to fire up properly in the Atari XEGS, I decided to walk away from the project for a few days. I was getting tired, and didn't want the fatigue to turn into frustration. At this point, I had invested almost a month of evenings and weekends into the project, and wanted to see it succeed.
A few days later, I came back and reviewed the design. The logic seemed sound, but I had questions. Putting the trusty LogicPort to use, I analyzed the signals of the 6809E and saw that the E and Q clocks were only oscillating when the TSC line was going up and down. The rest of the time, the clocks were dead.
Well, that explained why things weren't working.
I went back, buzzed through each of the connections, checking for continuity, rechecking the wires, and looking for shorts. Nothing stood out. I emailed the snapshot of the LogicPort to Gary, who quickly suggested where the trouble might lie. Sure enough, there was a short that I didn't catch in a critical juncture. After taking out the trusty Weller soldering iron and fixing that, plus a few more possible problem points, I hooked everything up and lo and behold, success! The 6809E was singing at 1.789MHz and running code consistently! No more wandering off when the ANTIC took over the bus. It finally looked like we solved the timing problems!