UPDATE!
It's been way too long since my last update. I've been super busy with work and family stuff and haven't had much good news to share.
The weekend after we got the engine in; Cam, Lachy and Morgan came over with the plan of getting it going.
We started out with something simple; bleeding the clutch. This turned into half the morning as it simply refused to bleed. We came to the unfortunate conclusion that the master cylinder is toast 
It's all the little things with these conversions that take the time. Cam was able to bring Geoff's (aka Guffry - thanks mate) MY02 Bugeye along as a point of reference. This turned out to be super helpful for things like vac lines wiring routing!
Unfortunately the car was having trouble starting. We were getting a battery draw light which we thought may be the cause but after swapping out the alternator with the Liberty one the light went away - WRX Alt looks like its cactus. But the car still wouldn't start 
After doing some troubleshooting we decided to call it a day. I suspected that there could be pin location differences between the JDM WRX wiring and the AUDM WRX manifold wiring.
I gave Miles at AM Auto a call for some insight and after some comparing of wiring diagrams, Miles was able to confirm that besides the lack of AVCS (on the '01 AUDM WRX manifold), all other wiring matched up. While this was a relief of some sorts, it still didn't shed any light on why the car wouldn't start.
Last weekend I set some time aside to do some more troubleshooting and go over anything I'd missed or connected incorrectly.
I managed to get the car started on starter spray which proved the engine was getting spark; it also meant that the cam and crank sensors were working properly (something I had suspected to be the cause). I also double checked fuel lines at both the tank and the manifold to make sure the send and return lines weren't mixed up; they weren't.
Miles also recommended checking the injector pulse. This can be done quite easily (and cheaply) with a 12V LED by probing the injector connector. I picked up a 12V LED from Jaycar for $3 which worked perfectly. This ruled out injectors too!
It's hard to pinpoint what the issue was but I have a feeling it was a connector at the back of the under-dash fuse box. It was plugged in but I don't think it was seated properly. There was a few other little fixes I found, but I don't think they were the causing the issue.
One thing I'm glad I found was this bent pin on the MAF:
I'm sure I would have assumed the sensor was dead when it threw a code I hadn't found this. The pin was easily straightened and plugged back in.
The exciting news is it runs!
I didn't have it running for long as the power steering pump is without lines and fluid but it was running well 
The only things missing now are a GD steering rack, pump, lines and a clutch master. I can then take it to get the exhaust modified to fit!
