Bad Pilot Bushing Symptoms?

Good Afternoon Everyone,

Ran into some issues with my Duster yesterday, and I am looking for anyone who may have had a similar issue.. This is the first time driving the car any serious distance in about a year - last year was quite busy planning a wedding!

First, a description of the initial situation and the problem:
1. Driving back home from work, 45 minute ride mostly highway, with no issues.
2. After cruising down some back roads, I notice it is a bit harder to shift than normal.
3. After about another 5 minutes of diving, a loud whirring / grinding noise would occur when the car was rolling, already in gear, with the clutch in. This noise would stop IMMEDIATELY after letting the clutch out.
4. I want to add emphasis - the noise was not when shifting gears, but after the car was already in gear and the clutch was still disengaged.

After I got home:
1. Removed inspection cover and checked for clutch disengagement when the pedal was pressed - seemed very normal, no sticking clutch.
2. Removed transmission and clutch. Clutch / pressure plate / throw out bearing seem perfect (they have less than 5,000 miles).
3. Transmission was difficult to separate from the bellhousing - I have installed and removed this transmission about 5 times, and it has never been that difficult, so I am reasonably confident it is not the bellhousing.
4. Pilot busing has deep rotational grooves - not linear "in-out" grooves from a rough install. No damage on the input shaft.

My theory:
I believe the pilot bushing was damaged by insufficient lubrication or grit getting into the pilot busing. Since the bushing surface was damaged, I believe that it was starting to "grab" on the input shaft of the transmission after long drives, which is why it was difficult to shift. I am hoping that the noise was the input shaft spinning against the damaged bearing.

Has anyone experienced anything like this?

Follow-up questions/remarks - this is asking a lot, but if anyone has any of this info from a past struggle, I would greatly appreciate it.
1. Input shaft has small amount of play - this seems normal to me.
2. Input shaft has tapered nose - this seems normal to me, but the taper may have been added by a PO.
3. What is the factory OD of the input shaft?
4. What is the factory ID of pilot busing?

Thank you!