Clutch linkage not lining up in neutral after shifting into 3rd

I stopped using the line up tool in the mid 1980’s. You’ve already found it doesn’t always work.

From your drawing (if that’s actually what’s happening you need to lengthen the 1-2 shift rod, or shorten the 3-4 shift rod.

I almost always make the rod that is shorter longer. It doesn’t take much.

Make it a couple turns longer and then check it. If its still off go one turn until you get the gate lined up.