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Ok I read through it and posted on the not need rejetting post, but I did not see anywhere if you checked for a intake leak?? I really would check that first, to ensure you are ok with the seals, then move on from there.
The 45 pilot should work fine, however due to the carb being a production item, many times the need to balance the transfer ports is needed. This is done by drilling a very small hole in throttle plate .050 up from transfers. This is one of many things I do when I prep a carb for a customer. Also check the pilot for any flashing inside the jet it's self as that will cause big trouble for you as well. YOu can use torch cleaning tool for this. Many times when the holes are drilled a small part of the brass gets lodged in the jet.
Swapping to a S&S is not going to help you if fact there are more trouble to tune , due to the fact they are only a 2 jet carb, verse's your 3 jet
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