Hi,
Are you able to place something like a long screwdriver through one of the bolt holes and manipulate the bell housing into position to get another bolt started? If you have two started on the driver's side, it should already be aligned. If there was only one, then I could understand why it isn't. By any chance, could you have started them in the wrong holes? Also, if you remove one on the driver's side, are you then able to start the passenger's side?
One other thought. Are you installing this with the transfer case installed? If so, you may want to unbolt and remove the transfer case to help.
If possible, take a couple of pics of what is happening and upload them for me to see. If the bolt holes are close, you should be able to use a screwdriver or something similar to align it.
I do have one other question. Are you sure everything with the clutch disc/pilot bearing is aligned and not preventing the transmission from pulling in close enough? You need to make sure they are. An alignment tool has splines that match the splines on the clutch disc and a pilot that fits into the pilot bearing. They need to be aligned before they will go together.
Here is a link that shows in general what I am referring to:
https://www.2carpros.com/articles/how-to-replace-a-clutch
Let me know.
Joe
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Saturday, September 4th, 2021 AT 10:15 PM