SE-1000 Maytag washer-Clunking sound only in agitation

[kav]

Hi:

I have a Maytag washer-dryer SE-1000, which is 31 years old. It has been a great machine for us and we want to keep it. I have done repairs on it over the years but nothing involving transmission or the tub's seals and etc. Lately the wash machine has been making a clunking noise only in the agitation mode. It also had an incident of a squeaking noise and a burning smell. I checked the belts and the pump belt was loose. I replaced the belt and the smell problem and the squeaking noise went away. However the clunking persists. The machine spins fine and drains fine. There are no leaks and it continues to do a good job with washing. I did the following:

1.  Removed the agitator and inspected it, it looks fine and not stripped. 
2. While the pump and motor were disengaged, I turned the drive pulley and I didn't feel anything that indicated a problem but then I am no expert!
3.  However, when I turn the pulley slowly, I could clearly hear the clunking, which seemed to come deep from the transmission.

I am concluding that something in the transmission is busted. So I have a question from all of you good people out there;

1. First of all do you think it is the transmission?
2. Second, I have to go the orbital transmission, because my present design is not available anymore. Will the orbital transmission replace my existing transmission, which I believe is helix?? 
3. Will my old agitator work? the newer agitator models that go with the orbital transmission, they don't sell their dispensers anymore!

Will greatly appreciate any input.

Best

Kav