When I bought my 1999 SVT, with 50000 miles, last year I had the same shifting problem. I first replaced the trans oil with the Ford synthetic, which helped quite a bit. However, the only thing I found that gives me consistent and reliable third gear shifts is to hold the gear shift in place until I've let the clutch completely out. This prevents the tranny from popping out. You can even feel it when it wants to pop out, which might be every 20-30 shifts. I only do this for the third gear shift. It's become a habit. Your not hurting anything (better than grinding gears), and it's a lot cheaper than rebuilding the tranny.
Marvin Stockman