Making a stroker would be a real cool thing to do. It is a fairly straight forward thing, you take a 258 Crankshaft and put it in a Jeep motor. You can also take the 258 connecting rods along with the crankshaft, but you would need special forged pistons then.
There are a lot of things to know before you do this, such as the crankshaft from a 258 engine is 1cm longer than the 242 Jeep crankshaft. So if you were to use your harmonic balancer from your Eagle, it would be okay, but if you were to use the Jeep harmonic balancer, you would need to make a 1cm spacer piece in front of the harmonic balancer.
You can use the stock Jeep camshaft and save a lot of money, but if you want power, there are performance 242 cams on the internet.
As for fuel injection, that is a hard thing to do (in my opinion). There are members here who have done it, and the person I recommend to ask is Tougeagle. I asked him once on how to do it, and he gave me a very detailed write-up on it. It would involve you putting in a crank position sensor on your transmission and tapping into your Eagle's wiring harness with a Jeep OBDII Computer, or other Fuel Injection software. But ask Tougeagle, he would know more.
EDIT: I would like to add that the Jeep 242 engine would bolt right up to your tranny, but you would have to make some adjustments with the battery tray. As the fan is offset on a Jeep motor, and would hit where it is right now on your Eagle. You would also have to use your Eagle oil pan, as it is specially made to fit around all of the four wheel drive hardware. You would also use your Eagle's motor mounts.
THIS SHOULD BE RESEARCHED THROUGHLY! Just make sure you do it right and on everything the first time! If you want to know more and read a step by step write up on a VERY successful stroker transformation, click here:
From Junker To StrokerYou can read this for more info as well:
Joshpit's 4.0L Engine SwapAnd this:
Can I swap in a Chrysler 4.0?