Don't remove the gravel.
You can replace the filter pad but I would NOT recommend you do anymore then that.
If you replace everything you've stated, you're going to throw your tank into another mini-cycle which will stress your fish out more then what they already are.
Nematodes are caused by over feeding and its not the nematodes CAUSING the sickness, they're just the byproduct of what's been long in forming.
The process I've come across is a long and involved, but doable one.
First off: Cut what you're feeding them by 1/3 to 1/2.
Second: Gravel vac your rocks. Only do about 20% of the water. You're going to do this every OTHER day for the next two weeks.
Eventually they're going to start starving to death because of lack of left over food and you're also pulling them out every time you clean the rocks.
This is a safer, less stressful method then removing all the rocks and changing all of the filters. Not to mention, that may or may not even remove all of the nematodes and if it doesn't you're out money on new rocks.
As for the gaping wounds. I always recommend using Melafix. It's a seven day treatment that you can do in conjunction with the gravel vacuuming. You just need to remove the carbon.
Good luck!
