If you have a flare, it's possible that your "local tranny shop" didn't install the correct thickness of spacer shim on the overdrive apply piston. This is in the rear section of the transmission so the whole tranny doesn't have to be removed to work on it, however, it is easier to just pull the whole thing and work on it on the bench.
Every rebuild manual out there tells you to measure the direct/overdrive clutch pack and then install the correct thickness of spacer depending on your measurement.
The overdrive apply piston releases the direct/overdrive clutch at the same time it apply the overdrive/brake clutch. If the spacer is the wrong thickness, the timing of release and apply will be off.
It's also possible that the overdrive/brake clutch pack is not correctly installed so it's taking longer to engage the clutch pack.
One way to gather more information on the problem is to drive around with a gauge hooked up to the overdrive port and see what the pressure looks like when it's making the 3-4 shift.