Dodge Ram Sport 1500 V8 Shaking and Badly Running

I'm having issues with my 2001 Dodge Ram Sport 1500 V8.

When I start the pickup it shakes, pretty violently.  It still continues to shake when
you're driving.  When I would back out of my driveway and put it into drive, it would take
a few seconds to click into drive.  Then when driving it would "buck" a lot when you got
going.  The check engine light was on and sending a code about cylinder 4.

My boyfriend put a new distributor cap on it and it stopped bucking, but it kept shaking.   
Then we realized that there wasn't very much transmission fluid in the resivour.  After
he put the transmission fluid in, the pickup drove completely normal...for two days.

After a couple days, it continued to shake when I started it and drove.  He checked the
transmission fluid and it was low again!  He filled the transmission fluid again and it
drove fine for the two blocks I drove it home.  

That evening we took it on a roadtrip and it started shaking again and bucking really
bad.  When it's a little under 1500 RPM's it shakes and the engine just doesn't run right
at all and it bucks a bit.  I  feel that it's lost a lot of power as well.  When we got home
he put all new plug wires in and when I took it to work this morning it was still shaking
and just not running right.  Check engine light is back on and flashes when driving over
30 MPH.

What is wrong with this thing?!  Some suggestions would REALLY be appreciated!

Summary:
-Pickup Shakes, when idling and driving
-Engine bucks, sputters and has lost power
-Transmission fluid isn't staying in reservoir long, but it's not in a puddle under-neath
the pickup
-Put new plug wires in
-Check engine light is on and flashes at speeds higher than 30 MPH.