Help to read RC 2channel input and fulfill dream. Pics inside!

The question is how I should proceed to get the Arduino to give me the length of the low periods.

Have you read PulseIn tutorial page? Aparently not:

Description
Reads a pulse (either HIGH or LOW) on a pin. For example, if value is HIGH, pulseIn() waits for the pin to go HIGH, starts timing, then waits for the pin to go LOW and stops timing. Returns the length of the pulse in microseconds. Gives up and returns 0 if no pulse starts within a specified time out.

I was not able to get a stable reading using the AD, perhaps the AD-function is not fast enough?

One reading takes 120 useconds, you results should be acuurate down to this value. It's difficult to say more, as you didn't provide an actual code.
Only remarks I can guess, trys to set higher value, about 10% of pulse is normal for a duration measurements:

while (input > 60){} //wait here until low pulse starts <<<<-- about 10% from 3V signal.
start = micros();