Your louder aftermarket exhaust is just masking a lot of the noise you could hear with the quiet stock exhaustMy solution was to remove the heat shield on the stock muffler after thinking it was all clutch noise.
I did all the same things to the intake as listed in this thread.
When I tried an aftermarket exhaust , the noise nearly disappeared.
While installing the stock exhaust, I noticed the heat shields on the mufflers were not very secure.
I left them off and went for a ride, no more noise complaints.