I put a thread up about the advantages and disadvantages of this the other day when i was thinking about it. Have a look in the technical section for it.
Depends what's ct12 it is but I don't think any of them are the same downpipe/ manifold flange as a ct9. Rebuilt a Supra Ct12 at work today and it defiantly wasn't the same. My brother ran a ct12/ct20 hybrid on his old glanza. You should be able to run the compressor side off the Ct12 and use the ct9 shaft though however it wouldnt make that much difference. And you would need to modify the compressor cover a little bit. If you need any more info mate you're more than welcome to ask me! I rebuild turbos for a living you see ;)
Brakes wouldn't cause any issue with the turbo mate Sounds like boost is dropping off, potentially a weak actuator or boost leak? Could even have slight thrust play in the turbocharger causing it to leak on boost. Is there any smoke at all?