Why does a clutch kit come with an alignment tool?
On a clutch with a pilot bearing or bushing, the transmission input shaft has two places to fit. Its splines engage the center of the disc, and its tip fits into the pilot. The alignment tool temporarily stands in for that shaft while the pressure plate is secured. Once the disc is clamped in position, the tool comes out.
Two tools on the workbench
Imagine two alignment tools that both slide through the hub of a replacement disc. One has a tip too large to enter the pilot bushing. The other fits both the hub and the bushing. Looking only at the teeth, you might pick either one. Checking the tip reveals which one can hold the disc on the same centerline as the transmission shaft.
If the transmission stops short during installation, a gap alone cannot tell you why. Check the tool and disc against the application, then follow the vehicle manufacturer’s procedure before attempting to seat the transmission. Using the bellhousing bolts to pull it into place can damage the disc.
Manufacturer references
Advanced Clutch Technology · AT25 · Valeo · Truck Clutches Service Manual