It takes less than an hour and a half. It should take just under an hour.
Shuttles are terrible (and they're dangerous)
JFK AirTrain to Jamaica and the E train to 42nd Street is definitely the way to go.
Fare control for the JFK AirTrain is handled at Jamaica. There are uniformed people there to help you. Don't worry.
The JFK AirTrain is very well-marked. There are audible announcements and digital displays telling you whether it is a Jamaica train (which is what you want) or a Howard Beach train (which you don't want).
Don't stress if you get on a Howard Beach train as it too connects with a subway to 42nd St. / 8th Avenue (it just takes a little longer).
This is all very well-marked / safe / user-friendly
At Jamaica, after paying the $5.00 fare to exit, follow the signs to the E train (big blue symbol for the E train). Here's a tip for paying your $5.00 JFK AirTrain exit fare - up to four people can share one MetroCard so no need to pay $1.00 fee for the card more than once. Also note, purchasing the $5.00 MetroCard from the nearby newsstand saves the fee. Newsstands don't charge the $1.00 fee. Please don't ask me why as this mystery is still beyond me. Why you pay a fee to purchase directly and why you don't pay a fee when purchasing from a third party ... mystery to me.
You'll be boarding a Manhattan bound E train in the direction of World Trade Center and exiting toward the back of the train at 42nd Street / 8th Avenue - very well-marked.