2000 3.8 automatic.. 3rd to 4th shudder and drivline vibration

I own a 2000 Mustang convertible that has approximately 190K on in and this car I just recently purchased, it has an annoying condition where when accelerating moderate to heavy the car will shake at 40-45 mph shift point for the 3rd to 4th gear, this occurs after going from a dead stop only,will not happen when making turns without coming to a full stop but only after a full stop... also I have noticed this is a recent observation after I replaced the right side header that was noisy (typical 3.8 broken header) I was revving the engine and noticed the same vibration was there at about 2500 rpm... I was told initially it was a torque converter, I added the additive from NAPA that was supposed to eliminate trans shudder but it hasn't helped, one last thing this condition is worse when the a/c is running too... I am dumbfounded and cant figure this out I have eliminated the basics such as tire balance and wheel runout I am a service manager for a large tire company so all the basics of vibrations have been covered... please help Thanks

I've got a 94 3.8 and had same issue, I went ahead ava and changed both universal joints which were only 20 for both and I changed out my transmission tailshaft extension housing bushing at the same time abd now doesn't shake at all you probably have it fixed by now but maybe this will help others, shade tree mechanic