Hello! I'm a total newbie to forums so I hope I'm not ...

My son and I bought a 2006 B3000 V6 3.0L automatic with 148,000 miles a couple months ago. He drove it with no problems for a few weeks before needing to register it, and then realized it didn't pass emissions. Turns out the check engine light does not work. There were several O2 sensor codes. We inspected the underside and realized the catalytic converters were missing and there was just a straight exhaust pipe instead. We ordered the cat online and installed it (my son did) with a couple new O2 sensors. The truck passed emissions and ran fine for the next few days, but gradually started sounding louder and ran more roughly (low power, loud engine, irregular). The computer showed several cylinder misfire codes. Then it sat for a couple weeks and wouldn't start until I had a mobile mechanic look at it - he identified and replaced a leaking passenger side exhaust manifold and found all the spark plugs were very dirty and fouled. With new plugs it started but ONLY with the ignition coil wires in a different configuration from the original (see below). Researching online I found that the firing order is 1-4-2-5-3-6 and I see TWO different coil configurations:

3 - 6
2 - 5
1 - 4

AND

1 - 5
2 - 4
3 - 6
The second one is the order I have them in now - see the picture. It still runs rough with low power e.g. very slow up hills, sluggish acceleration. I replaced the fuel filter (no change). I checked the coolant (no oil) and the oil (no water).

Does anyone have any ideas that may help us move forward? Thank you so much.