03 Ram 5.7 Hemi problems.

Correct me if I'm wrong, but that should have the dual plug heads with one plug having a coil pack and the other getting spark by a plug wire running from opposing cylinder? If a pair of wires are crossed, may do this and not throw a code. Also, the condition of the wires and the boots on the coil packs is something to look at. Had similar issue develop with my 05 Hemi Durango. Had a low rpm miss, but no codes. Threw plugs, wires, and boots on and we're good again.

Correct, the first few years they had that goofy cross plug wire sets, until they went to the dual coil on plug in 05 ish. The thinking being that if a coil fails...you don't have a complete cylinder failure, you only lose one plug, on two cylinders. Many prop airplane engines are like this.

anyways, alot of hemi swap guys that got stuck with the earlier coils just put these mini wires on them (see link below), to jump the coil to the cylinder it's actually mounted on. I also have seen truck guys use them. I'd say it's worth a shot for $45. If you do plugs, good luck on cylinder's 5 and 7. Complete pain. probably should have done them when you were doing the gaskets.

http://www.summitracing.com/parts/tay-72641/overview/make/dodge
They also have black and red, but they are 10 bucks more.