Okay, Matt is taking care of me and getting me the parts I need by the weekend - thanks Matt. Have I mentioned how awesome his company is?
I thought I would provide some notes on last weekend's progress while everything is still fresh. I apologize if it seems a little scattered but I wanted to get the information down and I can clean it up as the project gets completed.
Rear diff replacementl
This was initially a real PIA. I had asked about dropping it without touching my suspension and was told that I could. This is likely true, but I didn't have the car high enough in the air to let the axles come all the way out. As a result, we got it part way out and after pushing/pulling/wiggling for a bit I decide to just cut one of the axles. I apologize to the Subaru gods for cutting a perfectly good axle, but there comes a point where you get frustrated and just do it....
Putting the axles back in was not going well at first. We put the axles in and then tried to work the diff up into place - this just didn't work.
So, what we found, just remove the single long bolt that connects the lateral links to the hub. This will provide ample play in the hub to swing it up and out of the way making installing the axles after the diff has been re-installed to the car. I wish I'd done this from the get go as it's super easy and makes it all go very quickly. I didn't have to touch any of the other bolts on the strut attachment or the trailing arm.
Many of you probably already know this, but I didn't and hopefully someone will learn from my mistakes here

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Matt had kindly marked my axles with a left and a right tag. I took left to mean drivers side and right to mean passengers side. Axles went in without a hitch and sealed great along the diff.
Electrical Wiring
For many, including me, I was a bit worried about all of this as I can be a little dense sometimes on electrical stuff. There's also something inside that says I shouldn't be cutting factory wires around things like the ECU.
That said, this really was pretty easy. I snipped the identifier pin on B48. This wire was black with a white stripe. I then snipped the neutral indicator wire on the blue B38 (? need to check my notes or page 1 of this thread). The pictures Josh has on his website show this plug very well. Both this plug and the ECU were very easy to get to with the lower panel removed.
Next was the tranny wiring. Taking the 12 pin connector that attaches to the tranny, I pulled the wiring loom off to expose all the wires. I then shorted pins 11-12 together, soldered the joint and heat shrinked it. I then tucked all this back up into the wire loom. I then committed the car to be only a 5mt by cutting through the 16 pin connector wire bundle. It just cleans things up in the engine compartment and makes moving wires around a bit easier. I don't believe this will come back to bite me in the rear.
I have an extra connector from an 4eat tranny, thank you Todd, that I then got ready to splice onto my 5mt tranny. I didn't splice things up because I only have two 2-pin connectors to work with opposed to a single 4-pin connector. Until I get the tranny in the car and shift it around, I'm not sure which is the neutral and which is the reverse. But this should be easy.
I did not work on the cruise control. My C/C hasn't worked in over 1.5 year and while I miss it - it hasn't been enough to spend the time to fix it. I actually went ahead and pulled the pump and actuator out of the engine compartment this weekend to continue cleaning it up.
I will note, and this is important, when reading the pin diagrams - they are numbered such that you are looking at the back of the, i.e. the wires going into the slots. I discovered I was reading them wrong after I snipped the neutral indicator wire and then went to snip the ECU identifier pin only to discover there wasn't a wire at pin 20... which is why I never snip wires right up against the connector and leave myself room to splice it back.
Tranny Mount
This started out pretty easy. The AT mount is a single horizontal mount with three bolts on each side going into the chassis. The MT mount is the classic H-brace that has two bolts going into the chassis where the AT mount goes and then the other two go into the chassis up beside the lower control arm mount. I had to scrap away years of icky and sticky goo to get to a clean metal surface. However, Subaru did install these nice little plastic plugs in the bolt holes to keep them clean. Just clean it all up, pull out the plugs and you're good to go.
There is a note here to pay attention to - the forward tranny mount bolts are larger than the rears. This means that unless you have extra misc. metric bolts laying around you won't have what you need to install the tranny mount. I don't know what size they bolts were, but they are a step up in dia. from the rear bolts. Somone may be able to chime in here. I *think* the bolts I used came from the top back seat seatbelt mount.
Unfortunately, I ran into a large problem installing the mount. As I was putting in the driver's side front bolt, the welds holding the nut to the chassis broke. This occured before I was even really torqueing it down. It was starting to get tight and then *pop*, it started spinning. My friend and I are still trying to figure out where we want to cut into the car to weld this nut back. Right now we're thinking about using the small flat area just infront of the mount, it's located at the bottom of the firewall basically.
Other than that hang up, the tranny install went great.
Shift Linkage
The shift linkage I was given is from an 03' WRX. It dropped in with no problems.
There are a couple of notes here. You will need to take out the three posted torqx screws that hold down the airbag computer in order to get the AT shift linkage out. You don't have to disconnect any wires, just take out the three screws that are easily reach and then lift it up out of the way to get the AT shift wires out from under it. The other option is to snip the wires I guess, but I suspect that will interfere with things when you go to install the 5mt linkage. This is super easy, provided you have the right torqx bit.
The 5mt linkage drops right into place up top. Uses the same screws and everything. Underneath there is a place for the linkage bracket (I don't know the proper name) to mount and the threaded holes are already in the chassis. The pictures I'll be putting up later will clarify this. You will need a few bolts to put these in, so again, if you have misc. metrics laying around you're in great shape. Otherwise you'll need them. I'm sorry I don't have the bolt size, but it took a 12mm socket FWIW.
Do make sure you have both tranny connecting/shift rods above the tranny cross member before you bolt things down in the cabin. Otherwise you'll have to do what I did and undo the bolts up top to get the clearance to move things were they need to be down low. This is pretty minor, just a note as something to watch for and save yourself 5 min.
Well that's all the time I have today at lunch. I'll try to get some more up tonight or tomorrow. Once this is all done I'll have a lot of pictures to share as I've been snapping a bunch.
Again, thanks to everyone for the help so far and if there anything in my description above in this post that is incorrect - please let me know.