Pedal feel after Big brake upgrade

Yeah this will be caused by the larger willwood fronts and master cylinder size. Basically because your master cylinder is pushing the same amount of fluid as before (i.e. becuase its the same size as before) but now becuase your proabably got 4 pot calipers, with a larger overall volume, you need to push more fluid to get the pots to move the same amount as before. Overall on the track because your front to rear brake bias has changed without an adjustable brake bias setup you will take longer to stop than you did off the stock setup too. Your brakes will be out of balance front to rear currently.

Yes i have tried alot of different master cylinders and the 1 inch paired with as late a SW20 booster you can get gives the best all round result when using bigger callipers.
 
That being said anyone with a SW20 that wants the best out of their brakes should be using the GEN3 master cylinder and as late a brake booster as they can get as a minimum setup.
 
Besides the "feel" did everything go ok with your brake fitment Chausta?

Can you take a picture of your brake booster and master cylinder please.
 
If you have a early model you should have a slim GEN3 booster and master cylinder minimum. If you have a early model i suggest the 1 inch master cylinder and late booster upgrade.
 
Glad installation was a breeze for you.

I changed to gen 3 master cylinder and it is juat changed the pedal feel but not the braking. But my kit was designed to be used with a standard master cylinder.

I may be encroaching on sacred territory here, but I recommend an article on brakes called "Pulp Friction", published by Grassroots Motorsports, which clears up a whole bunch of things about braking.  A link to some jpegs of the article is given below, but it is easily found elsewhere on the web too.
 
There is much more to improved braking than simply upgrading to 4 pots calipers or using bigger discs.  For instance, I was about to embark on a popular upgrade to Mazda 4 pots with big disk etc. on another car I own, but fortunately read this first and then ran the numbers.  Turns out my braking force would have been within a few percent of factory spec due to a combination of different piston sizes, center point of the clamping force on the rotor etc.  I would have needed bigger wheels to fit it in, and loads of cash to do it all.  The only improvement I would have gained by this upgrade (apart from street cred) was greater ability to absorb heat, which I don't need a lot of on a street car anyway (racing is another matter of course).  So in the end I didn't do it and saved a lot of money, some unsprung weight, and no doubt grief fitting them.
 
Heat issues aside, the number 1 way to improve braking is actually to fit better tyres, as they are the bits that do the stopping.  Changing to six-pot calipers and the biggest vented, slotted and cross drilled discs you can fit won't help a bit if you're running skinny tyres made from rock hard compound.  Often what people perceive as improved braking actually comes down to different pedal feel.  That's not necessarily a bad thing either.  The brakes on one car I have bite far too soon, and on another too late, so I'd like to change them both!  But, if you can lock your wheels up (ignoring ABS of course), you've obviously got enough clamping force on the disc for the tyres fitted.
 
The article is close to the bottom of this page:
http://www.myturbodiesel.com/1000q/brake_FAQ.htm
 
I'm not trying to rain on anyone's parade or start a flame war; I think big brakes look good too, and if that in itself is enough reason for someone to choose to upgrade then I say go for it.  Understanding the physics of how braking works might save you some money and aggravation though, so if you are interested, have a read.

I have bled the brakes a third time and they are working perfectly fine now.

I will have to agree with a big braking kit doesn't improve your braking distance. But I knew that may have been the case before I purchased it. I upgraded because it was only a little bit more than the costs of rebuilding the standard brake system. Plus I get bigger rotors and some bling 4 pot calipers.

FYI I used stock brakes with EBC red pads in my ST185 at the last MR2 Challenge event and my EVO mate couldn't believe how late and hard I was braking with them, and they didn't fade once.
The only actual benefit you'll get with upgrading brakes to a larger size and/or calliper on a road car is that they look better!
All you need to do is make sure your rotors aren't worn out, your callipers aren't seized or leaking and that you have good pads and fresh fluid.