Can't think in a million years why anyone would want to put the 1.6 Turbo engine from the gen2 MCS in, it is dogged with problems.
As above, go for the gen1 supercharged engine conversion.
As for brakes, I believe that the gen1 JCW brakes fit straight onto the gen1 One/Cooper/CooperS (although I think you also need the caliper carriers too).
Also, I believe gen1 JCW calipers are the same as gen2 MCS calipers.
What he said.
2004 MCS JCW, 15% pulley, Dinan CAI, MSD ignition & wires, Mynes V2 header, TSW rear control arms, H-sport front and rear sway bars, H-sport lowering springs, Powerflex bushings all around, modified Forge intercooler, M7 STB , ATI Damper