input shaft doesn't move. If it does then you have serious gearbox issues. If you got the box bolted on correctly then it is seated correctly in the spiggot bearing. The throwout bearing shouldn't cause the issues you are describing. If it is too big then you wouldn't notice it and if it is too small then it could be forced through the fingers which would be greater pedal travel but these are unlikely.
What is the pressure plate like? Is this reused as it is likely that this is your issue. Other thing to check is that the slave cylinder has full free travel without pressing on the clutch fork but be careful that you don't overextend it as you can damage the seal. Next thing to check is that the adjustable rod between the slave cylinder and the clutch fork is correctly adjusted. If these are ok then it is an issue inside the bellhousing and first suspect is the pressure plate.
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