Because the scabs are part of your skin and would be painful (and even slightly dangerous) to remove, they are not considered a chatzitzah. They should be soaked well to soften as much as possible.

The degree of contagion via the water is rather small, but to be on the safe side, you should ask to be the last woman to immerse for the day before changing the water. You need to discuss this with the mikveh lady in advance, as different mikvaot change the water at different frequency and/or have filtration systems.

Refuah sheleimah!