The new input shaft I received does not match the original. Just wondering if the original is correct or is it possible someone machined the spline down for some reason?
They are the same length but the splines are shorter on the original. When searching images I do not find one that looks like my original.

 

More info:
Can we assume this is for a OEM Olds drive-train? 330-455...OEM bell housing etc...
What year do you believe the trans is?
Post the Muncie case ID. All of them, the main case, tail case, front bearing support, and fork cover.
Output shaft spline count?

Looks to me like that old shaft has been modified. Possibly for some funky stacked disc clutch?

Are you replacing the clutch? If yes compare the old to new clutch, disc hub and TO bearing stack up height.
Diaphragm style Ill assume. Verify the fork has full travel before stabbing in the trans. And the fork ears are on the right side of the TO bearing. (you'd be surprised how often that mistake is made, same for the direction of the disc).

Both shafts appear to have the right 10 spline count.
Both have the dual groove, though different. That generally indicates 66-70 wide ratio.

Here is a decent link with pics showing the different applications.

https://www.motortrend.com/how-to/18...-transmissions

 

Here are the pictures of the case. It is from a 1966 car not sure what kind. The one in my 65 cutlass had the syncros go bad so i was going to replace them but I was getting ready to leave for collage and I had never worked on a transmission before so my Dad found this one and I swapped out the tail piece because it had the speedometer on the wrong side. I may have swapped the fork cover also. Not really sure as this was around 1984-85. I do know that the linkage is from my cutlass.
Both input shafts have 10 spline / 21 tooth. output shaft has a 27 spline.
Yes I am replacing clutch and pressure plate. I am putting a new TO bearing in also. This is all going on the 455 that I have that I am going to start the rebuild after I get this back together. The 455 is from 1970 (VIN derivative 30M301313)

 

Your "original" input shaft has been monkeyed with for some unknown reason.
If all your other components: bell housing, throw out bearing, pressure plate, clutch, flywheel, crank and pilot bearing are all factory equivalents or originals the new input shaft should work fine.

 

X3, original shaft modified

 

Can you post a picture of your bellhousing and pilot bushing? I'm curious as to why it was cut like that.

 

Several engines ago, when I had a 400G with auto crank, I became convinced that the conversion pilot wasn't deep enough into the crank flange. It kept knocking the thrust bearing out. I almost turned it down in a similar fashion. In the end, I got a properly drilled crank.

 

 

I got the transmission from someone and originally installed it in my 350 that I had before the 455.
so it was cut before I had it.

 

Looks like a universal bell housing? Two starter snout holes.

The smeared main case number looks like 3885010 = Model year 1965 - 1967, M20.
P0301 is Muncie 4 speed, March 1st of 66.
The Vin stamp 6Z indicates 1966 Fremont CA plant. The last digits are the cars vin #s. But there is one too many digits there unless Fremont was beating to its own drum...again.
All this is off memory, so verify.

Check the flywheel to bell housing trans flange mount for concentricity and parallelism to the block & flywheel.
If that is all good install the bell & clutch and measure the stack up depth and compare it to the face of the trans and shaft.
There are YouTube videos showing how to set up your metrology and where to take the measurements.

If that checks, install the trans and see if it seats nice into the pilot and ensure the clutch disengages like it should.

Make sure you have the flywheel ground on a dedicated flywheel surface machine.

I'm at work, so I don't have time to run the case numbers.
There are at least two good Muncie sites that will break the numbers down.

 

Bruce @fleming442 nailed it. Your pilot bearing is not installed correctly. Chances are you have an automatic crank.

Pilot bearing should be recessed further as shown in the following picture.



From Joe P.
"MT on the left, AT on the right."