If you're going to go an SIDI Alloytec, I'd suggest using the LLT as it's got the older style headers, meaning if you wanted to do an NA build, you can get Paceys for it. LLTs are found in the 2009-2011 Series 1.5 cars. (those intermediate ones between Series 1 and Series 2). They're also seen in the 5th gen Camaros as well, meaning there's a ton of options for it. If headers aren't an issue the LFX would also be a great option since it's got built-in headers, meaning you only have to route a single pipe on either side of the engine for exhaust plumbing. Since that was also used in a Camaro, it's super easy to get options for it.
If you want a Manual (which, of course you do) your most likely source is going to be a wrecked ute. Utes are the most common cars to find manuals in. Although, you can't treat the Aisin AY6 box like a T56 or TR6060. (If someone could make a bell housing adapter, that'd be sick.)
Automatic wise, do not get a five speed. These boxes are absolute AIDS. (Hydraulic pump failures are the biggest cause of failure for these boxes since they're paired with an engine that puts out close to the maximum amount of torque that the 5L40E can handle) If you want to go auto, i'd suggest getting a 3.0L with the 4L60E from a Series 1 Omega, or a DI 3.6L and 6L50E from a Series 2. This means you'd most likely have to run the stock ECU as far as i know as it may talk to the Gearbox via GMLAN... Although, I could be wrong here.
As for DI ECUs? As MACE mentioned, MoTec works well with DI systems if you need something standalone. Not sure if a Haltech would work either, but Haltechs tend to work well with GM sensors, and many people tend to use them on LS swap builds for Jap cars. Although, whether or not they'll talk to a DI injector is beside me. Also you have to consider that an LLT has four variable cams with four phasers, so whatever ECU you do decide to use, it's going to be mucho expensivo as you'd need a shitload of inputs and outputs. LSs have much fewer sensors on them. As far as I know though, you'd have to run Manual boxes with any standalone setup.
The next issue would be getting engine mount adapters made to suit your subframe, and getting a transmission mount made. This engine's also much lighter than the Ecotec or the 5L, so you'd also need to get your front suspension retuned too. You'd also need to install a drive-by-wire pedal, somehow adapt the quick-release clutch line to the stock VS pedal (not needed if you're going auto of course), wire it all up, get a driveshaft made, and then pass it over the pits. You will most definitely pass seeing as the Alloytec has a smaller capacity, and is plain old newer than both the 5L and 3.8L. If your state has power to weight restrictions for swaps, swapping a VS SS or Statesman would be much easier since the 5L and Alloytec have roughly the same power output. Otherwise your tuner can do one dyno run to keep the feds happy, and another to keep you happy. (That's what one of my mates is doing for his LS swapped R31 Skyline)
Whatever happens though, this'll be a freaking sick build. Alloytecs are solid little engines when looked after, and being in a VS, you've got a somewhat lightweight frame with a decently grunty engine. You'll actually lose weight with the swap too, at least 60-80kg if you go a manual.
