But back to the scope traces (and thanks for the photos, they're very informative)...
STX direct is a 5 cycle instruction with 1 cycle of VMA low. The duty cycle on your trace is exactly that. Looks great.
STX direct should also have 2 cycles in a row of R/nW being low. You're not seeing that. We need to find out why.
First, please confirm that 0xdf, the STX instruction, is on the data bus (in the modified free run mode). All data lines should be high except D5. If not, transceiver U2 might be bad. To confirm, U2 pin 19 should be high and this should be disabling all outputs.
If you are getting 0xdf on the data lines, either the CPU is bad or something is forcing R/nW (pin 34) high. What I would do is try to isolate pin 34 by unplugging the CPU, bending this pin slightly, and plugging it back in leaving pin 34 hanging out. Some of the older ceramic packages won't tolerate this, so use your judgment and don't do it if you think it's going to break the pin.
If you can isolate the pin, hook the scope up to the pin directly and see if you get a duty cycle of about 40% on it (again in free run). If you do, next steps would be to find who's holding it high. If not, a dead CPU comes to the top of list.
Also, on your scope traces, that's a really ugly U15 pin 6 (signal: nEVMA). It looks like it's either driving too much capacitance, or the high side output driver is blown. We should come back to that, but let's finish with the CPU first.