I've put in hundreds of manual transmissions in everything that comes with a clutch. Test fit all your parts on the input shaft before installing them on the flywheel. That includes pilot bearing, clutch disc, and make sure the throwout bearing is the correct one as far as height/ GM has at least 3 choices depending upon what pressure plate you use.
It isn't at all far fetched for a clutch kit to have the wrong throwout bearing packaged, keeping the transmission from going all the way into the bellhousing. I've seen that scenario a couple times over the years.
I always put a light coating of grease on the input shaft and throwout collar, these parts need a little lubrication when assembled as putting it together dry will promote wear as time goes on. Just a light coating so it doesn't fly into the clutch parts, but will assist in sliding the parts together, and keeping wear at a minimum.
I've also aligned parts by eye, with a old metal input shaft, the new plastic tools that come with most kits, as well as wooden alignment tools, before plastic was a thing. The important part is making sure the alignment tool slides in and out like butter before attemting to install the transmission.
I never let the weight of the clutch disc hang on the tool when tightening the pressure plate. I support the alignment tool with one hand as I tighten the pressure plate. On tough installs, a couple pilot bolts (transmission bolts with the heads removed) are sometimes worth their weight in gold as wrestling the weight of a transmission over your head gets tiring quickly.
Sometimes when all else fails have someone else depress the clutch pedal as you wiggle the transmission that last little bit.
Over 50 years of experience of installing manual transmissions into trucks cars etc. Those are my helpful hints, I hope one of them is helpful to you.
