VF needs to write you a file with Stock software, rescaled for injectors, and a couple other tweaks to keep the DME fom freaking out with the blower installed. Then you can drive it (lightly) to set readiness. There are also a couple other tricks too.
Two things are common with a S/C or catless setup:
1. Oxygen sensor monitoring is NOT ready
2. Catalyst system monitoring is NOT ready
Everything else should pass but these two.
So - if you give me more information, I can help you. Which one of these is not passing readiness? Is it both of them? Or is it just oxygen that is not passing?
Let me know.