727 2-3 upshift VERY harsh

The kind of shift your describing is not a good quality shift at all. It is definitely not a race type shift. What is happening is it is overlapping while shifting from 2nd to 3rd. (It's slow coming out of 2nd gear while 3rd gear is already engaged thus it's overlapping gears). That's why you said it feels like you momentarily stab the brakes. Previous belief is the harder the transmission shifts the less heat it will produce and the longer it will last. This is NOT TRUE. A good shift is firm and will probably even bark the tires (depending on the rest of the cars combination) but it never jerks or feels like you stab the brakes. When it overlaps like this it creates more heat than a stock trans. ever would and it's as hard on a transmission (and other parts of the drivetrain) as it is for an engine to spark knock. Did they put in a 5.0 kickdown lever? If so that may be the problem. It doesn't usually work good with a manual VB. A 3.8 or 4.2 is the highest ratio that should be used. If a 3.8 or 4.2 lever was used it's possible the VB is defective.

I have one other question. You said you waited while they rebuilt it. How long did it take? I have been rebuilding torqueflites for over 25 yrs. and have all the necessary tools to do it quickly but the quickest I can do one by myself is approx. 8 hrs. If they did it in a hour or 2 it sounds like they did little more than a quickie rebuild (change the clutch plates and steel plates and maybe, just maybe replace the seals) and didn't take time to check any clearances (which should always be checked) and replace all the necessary parts required in a proper rebuild such as all thrust washers and all bearings. Did they install a bolt in rear sprague? With no low gear braking they should have or it can let the clutch drum over run and explode with the power of a stick of dynamite.

Also if a trans. is rebuilt and a manual VB is installed there should be no fine tuning required if the trans was properly rebuilt and modified. Only a stock type valve body with factory kickdown linkage will need fine tuning.