I'm so sorry to hear that you're having so many problems right now :( I think it happens to everyone at some point. I know I just finished battling some water issue that was causing holes to appear in my male's fins. Some salt in the new water seems to have helped tremendously. Also, my new tank is having an issue staying cycled, so I know exactly how you feel.
If you eventually want to switch the substrate you can do it up to half at a time and your cycle should hold. If you want to be extra careful do it in quarters. Just scoop out the old stuff and then put in the new. This can be done with the water and fish still in the tank.
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