Hi BGA,
When I said I have 2 back to back transformers to isolate the mains supply, it is so that I can check the operation of things like the pulse transformers, in operation. I imagine you are referring to the small pulse transformer/s used to drive the mosfet gates? I seem to remember seeing lots of small red colored pulse driver transformers in all the welders I have seen.
I seem to remember doing an ESAB welder, and the current transformer had broken loose and the winding had broken from the PCB. Just a lot of fiddling to get it back together and terminated. It was a strip wound secondary.
If the 'cycling' problem is apparent at 'idle' then you can use the isolation traffos to see what is happening. BUT if the problem is happening during welding use, then this is where the fun starts, unless you cannot isolate the control circuits so that you can get your scope to work on it.
I didnt scan through the manual I have to say, but I hope my comment helps you.
Now that I read your post again, have you checked through the current limit/current control section. One small welder I used to weld up an exhaust pipe was VERY impressive with its current control. I used a 2 mm rod to weld up some 18 gauge steel and it was easy to do without blowing holes in the steel. To me that would be the place to start. BUT, there should be output voltage on no load, yes??