Probably the reason it won't go the last inch is the pilot bushing isn't accepting the end of the input shaft of the trans. One can buy plastic input alignment tools(cheap) to help get this done, or use an old clutch shaft. Everyone should have one lying around.

Loosen all 6 clutch bolts, slide the tool in while moving the clutch disc around until the tool slides in all the way-Don't force it by beating on it with anything. It might take a few tries. As was suggested, make up some headless bolts long enough to insert through the trans. into the bellhousing to guide the trans in.

No reason to remove trans. to attach the if input shaft tool slides in. To line up the splines on the input shaft w/ the clutch disc, put the trans in high, so one can turn the rear u-joint flange on the trans. while gently pushing the trans into the bellhousing.

Good luck.

'37 GMC T-18 w/ DD 4-53T, RTO-610, 6231 aux., '95 GMC running gear, full disc brakes, power steering, 22.5 wheels and tires.
'47 GMC 1 ton w/ 302, NP-540, 4wd, full width Blazer front axle.
'54 GMC 630 w/ 503 gasser, 5 speed, ex fire truck, shortened WB 4', install 8' bed.
'55 GMC 370 w/270, 420 4 speed, grain, dump bed truck from ND. Works OK.