Since it will be a week or so, something I found years ago that is extremely handy is to get 4, 8" long bolts to screw in from the engine side to the bell housing mounting bolt holes. These are strictly to be used as guide pins and keeps everything lined up going back together. I don't have a clue what you have to work with, but I bought a Harbor Freight HD transmission jack years ago to drop manual transmissions out of my 1 ton trucks. It's been my "go to" tool for when I split the smaller Farmalls too. Not necessary, just super handy. A good sized floor jack works well too. The point is, something to adjust height of transmission when going back together. Even with the long bolts as guide pins you can see any difference between top and bottom mating surfaces from the side. You can eyeball it, or measure, whatever works for you.
If you use the pto shaft method, once you feel the splines make contact with the clutch plate, do not force it together pulling it with bolts or you can damage the clutch plate. At this point you can remove a couple of the long guide pins, and replace with shorter ones, but longer than the bolts that hold it together. Using the rear tires, roll/push/jiggle it back together. Here's where the top/bottom distance is important. If it's pretty close it will go together pretty easy. Tighten the shorter bolts finger tight to keep what you have and keep sides even. If you have a helper it may make it a bit easier if it's your first time. If it acts like it's binding a bit, once you get through the clutch disc, and starting into the pilot bushing, it's close enough together you can push the clutch pedal down to relieve any strain on alignment. The clutch disc just does fit in the flywheel recess, so it's pretty close to being aligned in place. But releasing the clutch will allow the tapered end of the input shaft to go into the pilot bushing.
And before going back together, take a smidge of good quality bearing grease on the end of your finger, and fill the dimple on the end of the input shaft to lubricate it inside the pilot bushing. This is assuming you're using no new parts as far as the clutch assy., or pilot bushing.
"IF" once apart and it looks like the pilot bushing needs replaced, you can use a proper sized bolt ( I'm thinking it's 1/2". I have an old bolt with threads cut off, and use the long shoulder of the bolt to use as a punch.) Pack the pilot bushing 1/2 - 3/4 full of grease, then smack the bolt/punch with a decent sized hammer. The hydraulic pressure should pop it right out. And if installing a new bushing, make sure to fit the input shaft in the bushing before going back together. I have an extra one out of a BN I bought for parts I keep around for this, but again a rod that measures the same as the input shaft will work. Seems a guy never has enough tools to make things easier, LOL...
.
I replied to a thread a couple year ago where a guy replaced the clutch assy., and pilot bushing. Apparently he'd smooshed the pilot bushing when installing, and sorta' forced the input shaft in it. Couldn't figure out why the clutch wouldn't release. Actually it was but the pilot bushing was tight enough on the input shaft, it was turning. Ended up having to split the tractor again to fix the problem. And these last 2 paragraphs are strictly for "just in case". Keep us updated on your progress..!!
*** One other thing came to mind, while you have it apart. If the input flange seal is leaking going in the transmission, might be a good time to replace it. Those drive flanges get a slight wear groove in them, and will leak if just replacing the seal. Found this out years ago, long before I knew they made those wear sleeves. Several places sell a kit (Pretty sure Steiner is one.) that includes the seal, and a speedi-sleeve that fits over the flange/yoke. seems they are around $35.00. And can be replaced the torque tube from the transmission about 4"-5". Another good place for those long bolts as guide pins. You'll need to disconnect the flex coupling from the flange. Just don't separate enough the input shaft drops out of the clutch disc. Remove the cap screw holding the flange/yoke onto the main shaft of the transmission, and pull it off (Mine came off real easy on the 130.) Then remove 3, 3/8" bolts holding the seal retainer on. Seal can be replaced on the bench, along with the speedi-sleeve on the flange. Kit came with a cup to drive the sleeve on, and a new gasket for the seal retainer. Again, this is a "just in case" thought while you have it apart.
I'm attaching a picture of when I replaced the one in my 130 a year or so ago. The one end of the sleeve has a bell shape to it, that in most cases is supposed to come off. There was enough clearance it didn't need to come off on this one, I'd imagine it'd be the same on a Super C.