Alright, I skipped the ignore and read this thread since it looked like a good topic for a tech thread that I could contribute to.
First, has anyone at C&C talked to you Dean? Dave was looking for an STi long block to prototype with... I dropped off my shortblock over there, but it's probably not that useful to them. I told Dave that you had a long block that you might be willing to sell them... so that may change your plans for your spare motor.
Either way, the issue with the motor AIMS built for me had nothing to do with AIMS. I reused my oil cooler (the small oil/water exchanger the oil filter attaches to) when I reassembled my motor. Apparently, no amount of cleaning will get all the bits of bearing out of that thing... so even though I cleaned the snot out of it, I ended up with dirty oil and that's what demolished my motor during break-in on the dyno. It was a nice $2000 mistake.
So, having had an otherwise good experience with AIMS, I would put them up there on the list of machine shops to go to for an STi motor build. You may also want to talk to C&C and find out who does their Porsche motors, as I get the feeling that a good Porsche shop would probably be a great currently untapped resource for Subaru motor builds, though they're probably expensive.
As far as building your motor: you basically get one (.020 over IIRC) bore out of the stock sleeves, which means buying some 100mm pistons. (Doing it twice means re-sleeving the block... which is why I ended up getting a new shortblock after my last one died because I didn't want to spend the money on potentially needing to sleeve my block and repair my crank.) I went with forged JE pistons and rings, ceramic coated, with stock base compression. That's what Mike at GST recommended. He might recommend going to a higher base compression these days if you're going to be doing the rest of the supporting mods like injectors, turbo, oil cooler, etc. I think that's where they went with the L at least. Higher base compression and a little less boost nets the same power with a more responsive throttle and earlier power.
I don't believe the valvetrain needs a ton of work unless you're going to go after a lofty redline. Even the Cossie heads use the standard style bucket lifters IIRC. They just up-rate the springs and oversize the valves, plus the port/polish. You can even run the stock STi cams in the Cossie heads and make 40hp over the stock heads. I'm not sure what the differences are between Cosworth's cam offerings, but I do know they're ridiculously expensive, and probably won't gain you much unless you're planning a GT53R or larger turbo, and a 9000 rpm rev limit.
Stock rods and crank are probably fine. People tend to break pistons, not rods or cranks. You'll just want to get them blueprinted and balanced, and have all the bearings replaced during the rebuild. I'm no expert on sizing, but apparently you'll want the motor to be a little looser than stock if you're going to run an upsized oil pump. This is where you'll probably want to trust your engine builder.
For oil pumps, I went with a JDM 12mm pump. Get it from JapanParts.com... there's a thread on NASIOC w/ the part numbers, and one of the members there works for JapanParts and was at one point doing a NASIOC member discount. The only issue is running the 12mm pump with stock bearing clearances... I'm not sure if the higher flow 12mm pump will end up just bypassing the oil because the crank doesn't flow enough. Either way, I'm not running a big redline, so I'm not too concerned. But if you're planning on going north of 7500 rpms, you're going to need to do some research about the larger oil pump, shimming it, bearing clearances, etc. Again, this is where your engine builder should be on the ball.
I believe the stock water pump is probably just fine. Though you'll probably want a bigger radiator and oil cooler.
Finally, you'll need to come up with something for the oil breathers... the GST tank I've got is nice, but messy. Crawford makes a decent, and smaller air/oil separator that breathes back to the intake. Plus you'll have to deal w/ the PCV and emissions crap (or just remove it like I did). If you're not planning on going too far past your current power levels, you may be able to get by with just catch cans... as the oil breathers will require you to change oil more often as condensation and exhaust pollutants don't always get removed from the oil and can drain back into the crankcase.