The input voltage to all the logic IC's come from the 5v regulator. If it is bad then all kinds of weirdness ensues. The step pulse signal comes from the optocouplers which will put out a nice pulse if they have proper voltage. The machine uses the chopper from (i believe) the x axis to feed the others. The l297's are made to daisy chain one's chopper to the others to sync the drivers. Also helps reduce noise.
If you shorted out the 5v reg and sparks flew from an l298 then I'd think that it was bad to begin with. Five volt regulators are cheap and easy to replace. Don't sweat it. There is nothing on this board that can't be replaced.
When testing an IC with a large open probe you might want to find an open test point in the trace connected to that IC like a via or a component with a lead.
As for the difference in the boards it is to be expected. My is from '05 and yours was pre-Light Machines. Even mine has components soldered between traces in places. After production 'fixes'. I've added some on my own components too. A few filter caps, a couple more biasing resistors, a 12v regulator to run a fan mounted on the l298's heatsink, etc.
I have no idea how the stock software will react to the controller not being hooked up to the mill but I'd bring the computer a long to your friend's house. Having the computer send step pulses to the machine while on the scope is the only way to go.
Let me know how it goes. Also double check your fuses