The MegaSquirt can do Alpha N (running on TPS alone), how ever with a small vacuum tank in line with the MAP sensor, I think you will be able to run it as normal Speed Density without any problems. However, I could be wrong.At least I know that I can have something to fall back on if I can't get it to run on the map sensor.
Yes, full standard loom and sensors. I ended up running 1 new wire seperate to the standard loom to drive the coil. The reason I did this is because I wanted to use spark cut for rev limiter, using the standard ignition system, the igniter is a smart unit, if it detects loss of signal from the ecu, it will continue to do the spark itself, but at 10' of timing. This basically overrides the spark cut, I planned to just by pass the igniter right up close to the unit but due to wiring diagrams of the igniter not making sense, I just ran a new wire.
So if I understand this correctly you did not use the standard toyota ignitor to run the coil. Does this mean that you can run the coil directly from the Megasquirt? Does it have an inbuilt ignition module?
Now, one thing to remember is that the MegaSquirt isn't a plug n play unit. There is a steep learning curve to them and there is a lot of documentation that can really overwhelm you when your new to it all. The MegaSquirt is cheap because it requires the user to do a lot more work, and sometimes you have to try things out for yourself as there isn't an ABC guide to doing it. I'd advise you buy a pre-assembled[url='http://www.diyautotune.com/catalog/megasquirtii-engine-management-system-wpcb3-assembled-unit-p-65.html?osCsid=e8da6b263be77a5437a8b9a1cbb4037f']MegaSquirt2 on v3.0 PCB[/url] and a [url='http://www.diyautotune.com/catalog/megasquirt-pigtail-harness-p-114.html?osCsid=e8da6b263be77a5437a8b9a1cbb4037f']18" pigtail loom[/url] from DIYAutoTune. If you ask nicely, they will probably even install the MSExtra firmware for you 
.I don't think i'll have a problem getting my head around it. I have wired up quite a few Haltech's before. The hardest part might be entering the settings into the ecu to get the correct trigger angles to fire the injectors and ignition
There is also a new option from DIYAutoTune, it's there own rolled version of the MicroSquirt but in a form factor for PlugNPlay (PNP) applications. They have one for the Toyota based on the 52-pin ecu's located [url='http://www.diyautotune.com/catalog/diypnp-nippon-denso-52pin-unassembled-kit-p-390.html?osCsid=e8da6b263be77a5437a8b9a1cbb4037f']here[/url]. I've no experience with these unfortunately, so you'll be pioneering it yourself This sounds pretty good too, I would presume that all the ECU's with this plug run all the same wiring pins or either you have to wire them up to suit your wiring loom. Now that you have thrown this into the mix I am liking the idea of a plug in ecu, so that if ever the cops defected me I could just swap the factory one in and away you go!
If you still have your stock motor in the car, buy the megasquirt and get it running on the stock motor first, this gives you a chance to work on an easy, already running motor that is problem free. Once you've had a few weeks of tuning and setup up the stock motor, you should be clued up enough to tackle an exotic balls out 4AGE Yes this is exactly what I intend to do!