[HSSS427]

You don't have to be overly gentle with it and it will take some jiggling around to get it to line up. Did you use a clutch alignment tool to make sure the hole in the center of the clutch was aligned with the pilot bushing? If the clutch hole is off center, you won't be able to get the input shaft into the clutch and pilot bearing.

Try to get a good sense of the depth of each section of the input shaft and where it has to engage with the clutch and then the pilot bearing/bushing. The nose of the input shaft will only engage the pilot bearing/bushing about 1/2 - 3/4" at most, so if you're 1 1/2" out it's likely you haven't gotten the input shaft splines lined up with the clutch splines. If the tranny is in neutral, the input shaft will spin pretty easily or you can turn the crank a little bit to get it to line up. You can also twist the tranny case around a little to get the splines engaged.

Getting the end of the input shaft into the pilot bearing/bushing is usually the hardest effort. It should be the last 1/2 - 3/4" of movement forward. So try to get to to a point where that's all the gap you have between the tranny and bellhouse. You can then thread the 4 mounting bolts in to help align the tranny and bellhouse. You can slowly tighten the bolts to pull the tranny into the bellhousing, but have to be a good judge of how much effort it's taking to close the gap and pull the tranny up tight to the bellhouse. It should mate up with out overdue force to turn the bolts in. If you find youself really having to crank down the bolts to pull it forward, then that's a warning sign. Back it out and once again get an accurate measurement of the distance from the bellhousing face to the back of the pilot hole in the crank. Then compare that to the length from the tranny face/spacer plate face to the end of the input shaft. I've used a long ratchet wrench extension and placed it into the bellhouse as if it were the input shaft, and then lay a straight edge across the opening of the bellhousing and mark the extension where it comes out of the bellhouse. You can then measure the length to the mark you made and then measure the input shaft. Then distance will be close, but the input shaft should be about 1/4" shorter.