So what you have is a hybrid between part of the schematic and part of the universal.
How are at reading schematics? I don't want to be condescending, but I also don't want to assume anything.
Based on you statment that you have the stock dash harness, I think the right side of the first image is factory and the left side is new. Is that correct?
Bill's highlights show the output side of the wiring, but not the inputs to the turn signal switch.
Can you tell us what all the lights do with the switch in different positions?
Can you also tell us exactly what aftermarket switch you have? Make/model/number/etc?
My theory is still that either the switch is miswired or the switch is bad. If you can give us the info on it, we can help look at it further.