Wonder why you think the bellhousing is off.

More likely you do not have the clutch disc centered up.

I usually install the clutch, PP and bellhousing with the clutch fork and whatnot all set up, slide the trans in as far as it will go and if it will not completely go in have someone step on the clutch pedal and it'll release the pressure plate allowing the disc to center up.

They say there are no such thing as a stupid question.
They say there is always the exception that proves the rule.
Don't be the exception.