If you're real serious about tuning, especially if your going for high boost pressures, I don't know of any reliable and cheap way to do it. You're going to want fuel and ignition tuning. I guess you could get a cheap fuel tuner and a MSD ignition. But for me, I wanted a reliable full stand alone management system. So you're looking at Haltech E6 or E8 or E11, AEM or Electromotive TEC3. The Haltechs and Electromotives are built for racing and require a custom installation. It can be done but requires a lot of work. There might be some custom installation kits for the mk III now, but a few years ago there wasn't.
The Electromotive TEC3's ignition is accurate within 1/2 degree or crank rotation. But it has that darn trigger wheel that has to be mounted on the crank and of course the Electromotive ignition coils you'll need to get custom wires. From what I've read and seen on other sites that offer the TEC3 and Haltechs, the TEC3 is the best.
The AEM is a stand alone that plugs right in to where your ECU is. It replaces the ECU. Its a little bigger than the Toyota ECU but will fit. It isn't as accurate as the TEC3, but will work with all the factory equipment. For street application, the AEM is the way to go in my opinion.
Of course these stand alones are $+1.5 K new and require a lap top to program. You might be able to pick up one used cheaper.
I'm in the same boat as you, I broke the piggy bank and got an AEM. Oh... the AEM support for the MkIII is real good. I wish I could tell you how it works, but I haven't installed it yet. I'm still working on the rebuild.
LoL
Let us know what you do.