Re: 4 speed saginaw noise
you removed the linkage, to get the transmission out? Or to slide the transmission to the back of the car to remove the clutch?
I have a 4 spd Saginaw in my 66' chevelle. I'm not convinced I know enough to accurately help you . . . did you change Clutch diameter? Resurface flywheel, replace throw out bearing?
When I did some some 'changing' on my transmission, like above, I had to spend some time readjusting the shifter.
Also . . . you didn't loose your clutch pedal return spring?
Now that I think about it, my Z-bar assembly might be over due for a rebuild.