Subaru engine swap problem

I am trying to put the manual transmission from a 1997 legacy outback and the engine (ej22) from a 98 or 99 legacy L into a 1996 legacy outback. Visually the engine and transmission look exactly the same as what I took out, I used the intake and wiring from the original 1996 engine and the only thing I had to change was the knock sensor. But, the engine and transmission do not fit all the way together, it will go to about the point of having a finger width between the transmission bellhousing and the engine and it stops and won't move any further. Does anyone have any idea why this doesn't work? I made sure there is nothing stuck between them, and that the clutch disc and pilot bearing fit onto the transmission separately,  but it still doesn't go together. I have taken the engine out of this car a couple times before (clutch, etc) and I don't remember it being a problem to reassemble. I'm about ready to pull the transmission back out and see if it will fit onto the engine out of the car, but idk what else to do. 

In reply to Tk8398 :

I remember Woody posted something about a weird Subaru clutch thing that caused a weird symptom. No idea if it's related to your problem, and sorry I don't remember a single detail, but maybe someone else here does. 

I'd pull it apart, pull the clutch off, then try to fit it together.  While you have it apart, check the OD of the transmission input shaft and the ID of the pilot (spigot) bearing, if that design has one.  Of course, that is all easier on the shop floor than laying upside down under the car.

Do you by chance have dowel pins in both the engine and the transmission? If so, pull them out of one of them.

Pete Gossett said:

In reply to Tk8398 :

I remember Woody posted something about a weird Subaru clutch thing that caused a weird symptom. No idea if it's related to your problem, and sorry I don't remember a single detail, but maybe someone else here does. 

^ That car was an automatic.

In reply to Woody :

Ah, damn...

I may have tried to install a Subaru engine with the dowels in both the engine and trans.  With use of some channel locks I didn't have to pull the engine back out.

My 99 to 2000 swap needed the knock sensor and wiring changed, also one had an extra hose in the air box to EGR plumbing.  I got real lucky with my junk yard engine, it had fresh head and timing work done already.

Is the pin still in the clutch fork?

Clutch disc is centered properly? Sounds like you are not centered on the pilot bushing.