3rd gear knock updated 6/1/12

[Kevin - Illinois]

The other thread was filling up... History - I started with a 31 standard coupe with a stock engine and drive train. The motor was tired and the rear main bearing failed last year. I pulled the motor and transmission and took it to a rebuilder in February. The motor was refreshed as a steel insert bearing long block with a 5.5 head. Since I had the car apart I took the transmission to the same person who rebuilt it as well. I am confident in the ability of the rebuilder as he has done many engines and transmissions.
I got everything together and started the car a little over a month ago. I made sure the entire car was assembled before starting it as I was told not to idle for the break in, but to drive the car (which makes good sense). I went through all the recommended checks including squirting a little oil in the cylinders the night before, pouring one quart of oil down the distributor hole, and loosening the oil pipe lower bolt to check the oil pressure.
On my first test drive the engine ran smooth in 1st and 2nd gears, however I did have trouble shifting into 2nd. The shift into 3rd was smooth, however when I let up on the clutch and pressed the accelerator I heard a knock at the rate of about 2 per second. The knock was in front of me, meaning it sounded like it was in the engine side of the clutch housing. If I pressed in on the clutch the knock stopped. If I decelerated the knock would stop as well. The knock is present only in 3rd gear.
I was told to the check the U-joint so I pulled the rear end and installed a new one. The knock didn't change. At the advice of good people I checked the starter bolts and they were the correct length and were not damaged.
I was also told that in the video it appeared the throwout bearing was riding on the pressure plate fingers. I checked and it appeared there was about 1" of freeplay.
It was suggested there was a problem with the throwout bearing hub. I dropped the rear end and pulled the transmission. I found no problems with it. I also checked the pressure plate to assure it was tight and there were no broken fingers. I also checked to assure the steel plate was installed for the flywheel bolts. I saw no shavings or indications of the bolts hitting the back of the engine.
I contacted the rebuilder and he mentioned he noticed and odd bend to one of the shifter forks when he rebuilt the transmission and that he replaced it. He felt there could still be a problem with the shifting tower so he shipped me another. I reassembled the car and installed the new shifting tower. The car shifted smooth in all gears however the knock was still present in 3rd gear.
The rebuilder asked me to pull the transmission which I did and took it to him. He went through it on the spot and found that the Main Drive Gear and the Main Shaft both had end play to the tune of .050. He corrected this and I took the transmission back and installed it. Once again the knock was still there in 3rd gear only and was unchanged.
I pulled the starter and installed a spare as it was suggested that I may have a broken spring. No difference. I jacked up one rear wheel and ran the car through the gears and the knock was still there but it may have been a little lighter.
The rebuilder built another transmission and sent it this week. I pulled the rear end again but this time I pulled the u-joint and test ran with the old transmission still in place. The knock is still there in 3rd gear only but it's much lighter.
Since I have the new transmission I will install it. I don't know what it means though that the knock is much lighter with the drive shaft disconnected.

Video of the knock...

https://www.youtube.com/watch?v=VMb7d...ature=youtu.be