Yeah if you replace your pads only, then they will have to break into the groves of your rotors. Whilst they are breaking in they will make grinding/squeaking noise. My bike did that when i put my galfers on. One thing you should do tho is take some brake cleaner on a rag and wipe your rotors down this will take all of the embedded brake dust off and they should quiet down a little bit. give em about 200 miles to shut up completely.
Clean the hell out of your calipers. Pull everything off, pump the pistons in a bit (not all the way) and use Bleche-wite and a tooth brush to get eveything clean. Then dry and push all the pistons back in and reassemble. This will give a clean surface for the pistons to glide in with the new pads. And yes, clean the rotors with brake-clean after deglazing them with scotch bright. Don't even think about using the old brake fluid. You need the lubicity of fresh fluid.
On another note - the stock 4 pad HH Tokico pads are just fine - even for extreme racing. The master should be changed out for a unit from a 06-07 (radial unit). Proper and complete bleeding is KEY! The second most important thing is PROPER BLEEDING. The third most important thing is no air in the system! Is this making a point yet? Two of my customers went through all the BS of changing out there 4 pad unit for what they thought was the plan with Honda and other 2 pad units. WRONG! When they rode my bike on the track and found out I was using stock pads and calipers - they almost had gave birth right there and then.