Does it do it in neutral? If it doesn't do it when you rev it in neutral, its highly unlikely its the engine (unless its a miss under load or something, which you should hear).
Also, if doesn't do it in neutral, rotating the converter probably won't do anything (and shouldn't), as the turbine and impeller(converter case) both spin with the engine. Now, the stator doesn't turn in neutral as it is what transmits the power to the input shaft. If locking and unlocking the converter makes a difference, you might be getting leaking in the converter circuit and it is trying to lockup but can't and causes a shudder as the TCC grabs and lets go. Did you damage the o-ring on the input shaft? I would be checking that if locking trhe converter solves the problem, I have had converters before that wouldn't go on without damaging the o-ring and I had to send the converter back and get it fixed before I could install it. Of course, if too much damage was done to the TCC by slipping it then eventually the problem will go away and the converter won't lock anymore.
If it does do it in neutral, I would looking at the balancer and flexplate to make sure the are correct for the crank.
Remember, in issues like this, it helps to figure out if the shaking is dependent upon engine RPM, tire RPM, driveshaft RPM (would be the same in 3rd gear), etc. And also whether t does it in neutral, or certain gears, or TCC locked, etc, accell, decell, etc. Good luck.