If it fully engages in gear and doesn't pop-out under acceleration, but when you let off the gas and it pops out... then I have your answer (because it's the same problem I have in second gear on my car!!!)
If you look at the shop manual (or Moss/VB catalogs) you'll see that there are two bronze bushings--one for second and one for third. These bushings get worn and start to have play. As soon as you let off the gas (or brake) the bushings slip and the gear pops out. The 3rd gear one is $33 and the 2nd gear is $25. I actually bought both locally from a TR mechanic coming through town for $25 total (lucky me.)
I'd talk to the shop that overhauled your tranny, because they should have checked for play in the bushings. The tranny will need to come back out and the bushings replaced. (There's no other fix other than to replace them.)
You can take the tranny tunnel off and then drive the car to the shop and unbolt the tranny cover. (6 bolts or so.) Then you can show the guys how much play there is and that it's something they definitely shouldn't have missed. Tell them you're happy to get the parts, but you want them to do the labor for free, since it's something they should have done in the first place.
Sorry for the bad news. I'm about to take the plunge and have mine fixed too.
Sam