Hello.
Our VNH5019 library does not use timer1 to produce PWM signals with the Arduino Mega. Instead, the library produces the PWM signal using analogWrite(). On the Arduino Mega, analogWrite() works with pins 2 - 13 and 44 - 46, so you should be able to remap the shield to use one of those pins to produce the PWM signal instead. Then you can call analogWrite() directly from the program and not use the VNH5019 library to control your motors.
Please note, analogWrite() produces a 490 Hz PWM signal. Some of our customers have modified our library to add support for using timers on the Arduino Mega, which allows them to produce 20 kHz PWM signals. You might find this thread on setting multiple timers for the Arduino Mega helpful.
- Jeremy