I have had it in and out ten times, but I can't get the shaft to go into the pilot bushing and close that last 1" gap. It's driving me insane...help please. I am exhausted! I have taken it all apart and reset the clutch using the alignment tool each time. I'm going to eventually stretch the bolts in the flywheel from tightening and loosening them over and over.

no idea.. try wiggling it?

I had trouble getting a manual tranny in on a Wrangler.
If you're 100% sure nothing's tweaked and perhaps have test fit the clutch disc over the input shaft, try putting it in gear and have someone push the clutch in as you try to slide it the rest of the way in.

As Carlton said just wiggle the hell out of it. Did you replace the pilot bushing?

What type of clutch alignment tool did you use? If you used the generic type, they sometimes do not get the clutch lined up right. I use the ones with the splines that look just like the transmission input shaft. I have had some luck by putting the transmission in gear and have another person stick the driveshaft in the back of the transmission and slightly turn it to turn the input shaft while I wiggle the transmission and push it forward. Also put a light coat of grease on the end of the input shaft where it goes into the pilot bearing.