I thought you had narrowed it down to the filter? Still playing up?
VR6, I don't have the locking tools or even the proper tensioning tool. I can see they would help, but I, like you, have always managed without them. You're right in what you say, its almost impossible to get the intermediate shaft in exactly the same place. I usually end up having to rotate the distributer body slightly to get it back to TDC and then of course its out with the strobe.