Changing the CPU cooler is a doddle and doesn't affect any warranties so there's no reason not to do that. A 5.25" bay fan controller would be a great idea for your case fans. 12cm fans at full speed are damn loud. With a fan controller you can slow them down to under 1200 rpm and they will never bother you again.
The X1900XT is another matter though since you probably lose the warranty by changing coolers. Whether it's worth doing would depend on how loud it is, I've never heard one. VF900 would be the best cooler to put on it, but if the card breaks and you need to send it back and put the original cooler back on there's the question of whether they could tell you had swapped coolers. Getting that sinks off the vram would be an issue too.
CPU/GPU coolers aren't just quieter, they also cool much better. VF900 takes 13 degrees and 4 dBA off an X1800 XT at idle, and 20 degrees and 11 dBA off under load.