What would cause a 1995 ford straight 6 to not fire right on every other cylinder?

The truck is a 1995 f-150 4x4 and its running so rough the engine is shaking

Do you know for sure that only every other cylinder is firing? Or are you just emphasizing how rough it is? Sounds like you have random/multiple misfires.

To start, I would make sure your ignition wires are going to the correct cylinders by following them from the ignition coils. If someone has changed the spark plugs/wires recently, it can be common to accidentally switch some. Someone could've done it just to mess with you.I've had a buddy do that to me before haha.

if that seems fine, I would check your spark plugs one by one. Check for them to be fouled or corroded.

Some more info would help. Does it run rough all the time or just at idle? Has it lost a lot of power, or just shake a lot?

Sounds like the plug wires are crossed.