1994 GMC Sonoma aligning transmission

Well the pilot bushing hole is about 1/2" deep.
If you have an inch or two to go.I'd says it's the splines holding you up.

When I did mine it took me a few tries too.
Even with the alignment tool. That only aligns the clutch center of the pressure plate.
You will have to turn the input shaft of the trans to line up the splines.

If you didn't use a alignment tool you need to take the pressure plate back loose and use one.
It will align the clutch with the pilot bushing and center it in the pressure plate.