from your descriptions first things i would do is take pressure readings
if engine is not missing or skipping why tune it up?
- take compression check on cylinders
- take pressure readings on hydraulic system
- take pressure readings on transmission @ the control valve (clutch, main pressure, torque converter)
- make sure the inching pedal system is adjusted correctly.
- you may have more than one issue with this truck being it has 12000 hours on it. it could be worn out
- the clunking in the torque converter area might be a broken flex plate so check it closely, or it may just be a clutch pack sticking or hanging up and then freeing itself up as you rev the engine.
you will find out alot if you just run pressure checks
there are tests that test it at idle and at high rpm... there ARE expected pressures at either low and high rpm.
just follow the testing procedures in the manual, if it does not meet the required pressure ranges at the expected rpm's you have a problem that needs to be fixed.
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