Neither of your sentences are grammatically correct.
It would be better to say:
There are many health problems to overcome. Each (one) is of vital importance.
There are many health problems to overcome; each (one) is of vital importance.
Overcome is one word (not two), and a comma is not correct here because a comma cannot be used to connect two independent clauses. You can either use a period/full stop or a semicolon (see this lovely infographic on semicolon rules).
You can also better understand why we would not use "are" in this context when we add "one" to the phrase. "One" thing is singular, so it uses the singular "is". Since we are talking about each health problem as individual problems, we think of them separately. Each one is vital, not the group of them all as a whole.
However, if we use an example from the Oxford Living Dictionary (as linked to in a previous answer by gusmog):
they each have their own personality
We would not add "one" here, so we would not use the singular "has". Try to pronounce "they each one has"; it is very strange to even read.
(This "adding one" trick may not be universal, but hopefully it will help you to understand.)