Well, I am not surprised. The Mini is entirely unsuited to the use of steel springs, and is critically dependent on the use of very non-linear rubber cones in compressive shear to get satisfactory operation within the constraints of the small amount of suspension travel due to the short wishbones.
The ONLY way of getting a progressive rate (and even then it will not be progressive enough) from a steel spring is to design it so that the coils gradually close up and make contact, so the operational length of the coil becomes less as it is compressed. There can be some kind of soft buffer between coils, such as spring assisters used on conventional cars sometimes, but generally, especially within the confines of a Mini, the turns just touch. Not surprisingly they may be somewhat noisy as they do that. It also results in damage to the paint or other coating, which encourages local corrosion and the resulting pitting leads to fatigue cracking. Variable rate coil springs in the environment under a car are a really bad idea.
Also you are probably having excessive and fairly violent bump stop contact due to the inadequacy of the springs. That may be noisy.
You can't change any of that except by putting the suspension back as it was originally and properly designed. However there is one more thing, did you replace the knuckle joints? These are not very expensive compared to the damage to top arms and rear radius arms that will occur when they wear through.