2007 Eaton Gen 3 Automatic Transmission

Does it have a pedal for the clutch, or one of those centrifugal type clutches?

 

All though I have no experience with heavy truck auto transmissions I do have quite a lot of experience with automotive automatic transmissions including the Alison units used in GM trucks.
With that being said I am thinking when you drop the transmission in gear (when working correctly) the input Shaft clutch should apply and the input speed should drop to zero RPM.
also when the smaller Alison units sense a slip or electrical issue many times they go in to inhibit mode
which doesn’t allow the engine to rev up or the trans go in gear.
Judging from the clunking sound you are hearing and the fact that you can’t get the input shaft clutch to apply it would definitely make me believe that you have an internal mechanical failure inside the transmission.

 

Where do you think the noise is originating from?
Front of trans or rear?
Unfortunately bad noises usually indicate internal damage of some sort.
Also I am concerned with the input speed not dropping to zero when put in to gear:
In the smaller units the input drum has a reluctor ring on the outside of it and a speed sensor that reads it thru the trans case.
Does this unit have a speed sensor just to the rear of the front bell housing?
Also does the trans gear position switch track normally with the scan tool reading?
And is your software an OEM type or generic?

 

We had one in the shop a couple years ago, and for some reason I seem to remember it made a clunk noise as the weights changed position once it started to grab or release at the point enough rpm caused the engagement or disengagement. Customer said it always did that. That's the only one I can remember ever seeing. If it won't get into neutral, then the clutch could be dragging, or the inertia brake not working to stop the trans. Do you have Service Ranger to see if there are any codes and monitor input shaft speed at neutral?

 

Yeah, never mind this, enjoy your vacation! LOL!