I had a mt on a subaru go bad. It had noises in certain situations. I taped a cell phone to the transmission and put it on record. U could definitely tell it was coming from the trans. Might try that.
How does the rpm react if you push the clutch to shift or just push it in? Like u said it will knock the cruise off if you hold it for more than a normal shift.
I am a 5G Ranger owner at this time. They do not offer a manual transmission and I don't like that. I'm checking out the bronco manual trans. Just don't see them at the dealer very often!