Our 1923 Model T has developed a clunk noise when I move the clutch pedal from low to high. Once in high gear, there is no noise and the car runs well and quiet. There is no noise when I push the clutch pedal into the low gear from a stopped condition. And there is no noise when I press the reverse pedal from a stopped condition. So I have ruled out the universal joint. Any suggestions as to what causes the clunk and is there anything I can do short of removing the engine and transmission.
Does it do it when the engine is not running? Have you removed the door and looked inside?
When you stop, the u joint and rear end is preloaded towards reverse. I suspect the noise is from a failed part in the rear end, or an unpinned U joint that has worn the drive shaft to U joint interface surfaces. Or a shot U joint.
Like Royce, I suspect the rear axle as a possibility. It's often the real source of "transmission" noises. Do you know if it's been rebuilt? Have you ever looked inside? Here's why I ask: http://dauntlessgeezer.com/DG79.html
We had a noise in the "transmission" and Lee Pierce suggested we listen with a stethoscope (?) with the car running. So Greg & I removed the flooring and listened at the transmission and then down the torque tube and sure enough it got louder as we moved to the rear! We pulled the axle and the pinion was shot.
Both the owner and the first shop were wrong about the "transmission" noise. The 'scope only cost a few bucks at Harbor Freight and it save far more than that on the first job.
A clunk like that is pretty normal if you are running "modern" clutch discs...
See if you have excessive fore & aft play in the torque tube ball joint. If there is too much play, (due to worn out ball joint clamp ring), it will clunk just as you describe.