My TR-3550 (smaller, weaker input and output shafts then the TKO) was pretty notchy at first. On the advice of a Tremec rebuilder I found on the web (not Hanlon, BTW), I changed the GM Synchromesh fluid after the first 1000 miles.
Actually, when the engine had only been run a few hours and scored the bearings, I pulled the engine and tranny out and the Synchromesh was filthy with many small grey AL chips (very little iron or steel, as hardly any of it stuck to the magnet I fished through it.) So when I reinstalled it, I used fresh fluid. At about 1000 miles, I changed it again.
The guy I talked to said change it after 1000 miles, and again after 2000 miles. My long trip to AL made be go past 3000 miles, so I'm due.
The Synchromesh is not cheap. But if it helps with shift quality to do that, I'm all for it.
My Tremec shifts very much better than when it was new or even had 1000 miles on it.
Of course, throw the stock shifter away and get a Pro-5.0.