Dick,
When we first got our 289 (used) it squeaked & groaned in the rear when coming to a stop. Knowing that it had been driven little, I lightly held my foot on the brake for several miles to let the pads scrub rust off the rotors and heat everything thoroughly. It didn't take long for the noise to go away.
On other vehicles, I have pulled the pads & rotors and basically just deglazed both with success. This consists of going over the surfaces with a Scotchbrite disc on a small rotary air sander. And yes, I did rough up the friction material on the pads this way to break the glaze. Just wear eye protection and a decent respirator. (Keep in mind this is on typical production pads, which have friction material over twice as thick as our Cobra pads, and hence last many more miles. On the Cobra, I'd just get new pads.)
As far as effort, the top thing you can do is break the pads in via the instructions on this web site (search will turn them up).
Another note about effort. I discovered that a great deal of the "poor braking" on these cars is a perception issue (at least it was to me). With the factory Wilwood pedal setup, I literally felt like I was going to push the pedal through the floor before the car would stop. Anyhow, I wanted to raise the brake pedal anyway, so I made up some extended clevises and installed them on the balance bar. The pedal came right up, and HOLY COW! The car stops so much better!
Now, I know good and well that raising the pedal didn't actually change the amount of leg effort required to stop. BUT - it put the pedal in a position that I am more naturally comfortable with. It now "feels" like the pedal in my Jeep, in my Chevelle, even like the one on our John Deere tractor! This feel is familiar to my leg, and so the PERCEPTION is that the braking is now much easier. Sure, the pedal position would be lousy for a real race driver who likes to heel-toe. But, I aren't one of those guys.
Anyhow, just some thoughts that might help.
Zach Butterworth
289 FIA #9367