I checked the calipers as that was something I suspected as well. However all appears to be fine there.

I was very careful about not running the master cylinder dry. I did however suck the old fluid out and replaced it with new fluid before we started bleeding the wheels. That shouldn't have introduced any air right? Is the only way to bleed the master cylinder to crack the line fittings?

I have not noticed the backs smoking but they get plenty hot. The ABS also kicks on the rear when the fronts start to fade.

What really has me perplexed is the system work well before I did the swap and under "normal" driving they work ok it's only when I step it up that the problems start. So I find it hard to believe that the master cylinder is bad but hey... Stranger things have happened!