If you're within an inch of going together, you're almost home. Apparently you are far enough together, you're through the splines of the clutch, and all that's hanging you up is the shaft going in the pilot bushing.
As mentioned, some longer bolts to act as guide pins works well to get you lined up. I'm not familiar with the 281, so not sure if they are studs, or bolts and nuts, or both. None the less, if you have some slightly longer that will reach, and help pull it together would be great. You don't want a lot of tension on it, and force it as mentioned, just keep it from getting away from you. Get several, 4 would be better..., bolts aligned. Check that the mating surfaces of the trans housing and engine are equal distance apart, top to bottom, even sideways. Your floor jack under the front will give you some adjustment. A bottle jack under the trans. will get it where it needs to be. Hence the reason for the longer bolts to keep it from getting away from you.
If it were me, and still had the come along hooked up, or bolts long enough to keep from losing what you have... I would put the slightest amount of tension on it. If you have a large wrench, ( I have used a smooth jawed Monkey Wrench) I would then release the clutch/pressure plate, using the arm the clutch rod hooks to. With the tapered nose on the shaft, and if it is close. With pressure released, it may allow the input shaft to align itself. A helper, or some good ole' enginuity to hold it there is a big help. There may be enough adjustment on your clutch rod, to let you hook it up. I have been known in the past to wire a clutch pedal down doing this.
You may also help it some, by putting the trans. in neutral, and engaging the PTO. If you have a large enough wrench to fit over the PTO shaft, (I believe an 1 1/4" will fit loosely, but a 15" Crescent/adjustable wrench works better) turn the PTO shaft. It may help it walk itself in.
If it still won't go, I went to AGCO and looked in the parts book. It does show an apparent inspection cover on the bottom. I'm not sure if this will allow access up through the housing, to the input shaft, and release bearing or not. If releasing the clutch let the shaft drop, as to where it is too low to go in, you may be able to raise it back up through that opening. A mirror and trouble light should keep you from getting under it, and see if you have access to move it. Some cribbing, a bar, and a narrow "1 by" on end, may allow you to raise it up.
On all of my older tractors with this type of PTO, that is how I get them back together... Trans. and PTO in gear, and use a wrench to turn the PTO. A 3/4" ratchet, and socket to fit the PTO is the berries. Once I am as close as you are now, I block the wheels from rolling back, put the tranny in neutral, and use the longer bolts to pull it together. Just a smidge of tension, so as not to loose what I have. Turn the PTO shaft, and it has always gone together... Again, it may take a little jiggle to get it to go...
Just be careful, and always remember anything can break... Don't get yourself, or apendages in a position you can't get out of. Especially if your working on it yourself... Pappy instilled that in to me many years ago. Just take a few seconds, and think what COULD happen, before sticking a hand in, or getting under something.
Sorry the post is so long winded, but "have been there done that"... Sure makes me appreciate what I have to work with now...
Good luck, and let us know how it turns out...!!