Megasquirt is pretty decent these days and can run just about any motor thats not direct injected. In the latest revision they can do DBW as well.
If you want i can help you plan it out or answer questions. I did a full MAF based sequential injection/ignition for my 240z.
If I get crazy a Twin turbo 3UZ swap might be in my future.
You should also look at LINK+ ECU A little more money but they do have some pretty good features, cruise control
I don't think any aftermarket ecu can do direct injection yet since its a bit more complicated and varies wildly between manufactures. Also the factory ECU have gotten much better in terms of hackability and tuning options.