So, did some more digging around with electrical issues resulting from the swap. Found quite a lot of strange things that I wouldn't have suspected from a Japanese car... Almost seems like Subaru made this exact project deliberately difficult – just for fun.
So here are the things that caschmidt and I noticed:
The cam timing sprocket, as Ben noted, was different. I had one ordered at the local dealer for a whopping $20. It certainly was much more intricate in design (read: more pulses/rev) than the automatic version. The FSM also shows the ignition system using these different versions, and strangely, the automatic (with it's simpler crank sprocket) also shows input from a cam timing sprocket. The FSM only
shows the crank sprocket on the manual, as if the manual doesn't use a cam sprocket and that's possibly why the crank sprocket is more complex.
Despite this, two or three manual 2nd gen imprezas in a local wreckers yard had the simpler
Also, found a strange reference to a pin on the ECU which supposedly is an AT/MT Identification pin – pull-up type, like that seen on the 2nd gens, ground the pin (which is internally held logic-high) and the ECU acts manual. Made sure the resistance to 5V logic high wasn't more than 1kΩ, it wasn't, so we grounded it. ECU immediately acted totally different. Didn't seem to stall or bog at startup, however caschmidt noticed that revs hung in-between shifts - as if the ECU were holding the IAC open... Also tried connecting and disconnecting this pin while engine was running, and each time the ECU responded by very clearly
changing idle, as if it were clearing adaptations and finding idle again, although either way it never stalled and seemed to idle smoother with the pin grounded. None of this makes sense since everything
I've heard point to the 3rd gen NOT using the same ECU for manual/auto. I've found plenty of differences - namely the ignition timing Ben mentioned, as well as the idle air controller, which is a simple solenoid on the auto, and a very German-like stepper motor on the manual. While I agree with Ben, that there probably isn't a "AT/MT Identification" pin on the BE ECU, I couldn't help but try as I mentioned. The pin referenced on the document I found was Connector B135 Pin 25. This pin doesn't appear to even be listed on the FSM I have for the car. It certainly does something, and it's definitely an input as the resistance is 2.01kΩ.
While I think that running a 5MT ECU is the best option, there's just too much
that's different. Idle air controller, sprockets, and a bunch of other random stuff I can't think of right now. Is it worth swapping the ECU if it means re-wiring lots of the engine electrics? This goes along with the ABS. The pump uses the same motor, but it's evidently got a different control module in the pump housing. If we get a new manual ABS pump, will it need re-wired or will the wires in place work? My assumption is no, since the speed signal is probably coming from the TCU in the auto and from the ECU/IKE in the manual.
Another question for any "Scooby Gurus" or others would be: What's a good option for a PC interface for module coding/re-programming? I've got a huge stash of interfaces for my Bimmers – from the old ADS interface to newer KKL and even D-CAN interfaces. Coupled with INPA/DIS/SSS it's an unbeatable and wonderfully powerful tool for this sort of work on a BMW. So many jobs have gone from teeth-pulling to piece-of-cake with a little software and the right interface. I'm still interested in using Subaru Select Monitor for some coding, but information on the interface to use is very sparse. The only thing I can find is that coding requires a dead-simple 5V TTL interface but reading DTCs requires a more complicated (similar to K-line?) interface... Does this mean I need two interfaces and have to switch them when coding and then reading DTCs? Much appreciation to anyone who can point caschmidt or myself in the right direction with regards to a computer interface for this "factory software".