The whole coilovers will work, front and rear. The "longer bolts" you mention are because the Si uses a different control arm, a hollow one thats lighter and stronger and uses a wider shock bushing. On your car, just use the front coilovers, NOT the shock fork from the 00 Si. The shock from the Si will go into the non-Si shock forks, and vice versa. The Si shock forks and LCAs should be considered a set.
The Si rear brake pads are the same for both cars. The front brakes are different and the pads won't interchange. The whole knuckle will though....but the 96-00 knuckles are 0.5" shorter, so you'll have fucky camber, unless you lower the car, then you're good, hehe.