Subaru EJ22 manual transaxle problems

I am trying to decide what to do about this problem, so any suggestions would be helpful.

I have a 96 Legacy Outback with 460k miles, its still in decent shape, and I recently replaced the engine with a used one from a wrecked car with 98k miles, replaced all the suspension bushings, ball joints, etc, so I would like to keep it for a while.  The problem is, the transmission is one that only came in a couple years of car (cable clutch with the old style bolt pattern and 4.11 final drive), and the one in the car was barely working anymore, and I have tried two used ones so far that were both bad.  So, which would be better?

1.  I have 2 broken transmissions (one with bad input shaft bearings, and one that is extremely hard to get into first and second gear) plus one in the car with failing output shaft bearings, so I could either try to rebuild one myself, or have someone do it.  I am not sure if enough parts are still available though, and how much it would cost.

Or,

2.  Get another used engine with the newer bolt pattern so I would have more choices of transmission, and swap to a newer EJ22 and matching transaxle.  The things I am not sure are how new an EJ22 can I bolt the intake manifold onto from the old one and use the same wiring, and will I need to swap to a hydraulic clutch with the newer style transmission, or does it work the same way where you can just move the clutch fork pivot to the other hole and still use the cable setup?.

Any ideas or other suggestions?  The work to do either option isn't that big a deal, and I think both would cost less than half what buying a newer legacy and doing the same work to it would cost.

In reply to Tk8398 :

It's a Subaru, an EJ engine will bolt to any EJ transmission. This link has more info (there are other available on Google). (there are pictures a ways down).

I looked all of this up when I bolted a 98 EJ22 5MT onto a 2002 EZ30D. More bolts, more better obviously, but for your purposes I think the 4 will be fine. 4.11 is also pretty common as a final drive, so finding a new transmission shouldn't be hard. This would also be a good opportunity to look at your gearing, 1st-4th are mainly the same, but 5th gear had some variation over the years. This link has quite a bit of info on various transmission options for you.

The cable hardware is interchangeable with the slave cylinder, the big difference is the clutch fork (which if you haven't replaced you should consider). The difference is where the fulcrum is, and having a provcision for the cable vs rod of the slave cylinder. I know in my case, I the box was already machined to move the pivot (it screws into the gear box), and the slave cylinder bolted up in place of the cable mount.

I know people do rebuild Subaru 5MTs, so I would give it a shot (because it seems cool), just maybe as a side project when you're not so under the gun.

So the later transmissions with more bolts will bolt to the older engine with 4 bolts with no problems? That definitely would make things easier. Both the clutch and clutch fork only have a few thousand miles on them so that should be ok.