Sputtering Backfire

Hi guys, my vehicle has a 4.3 V6 vortex engine in it. This morning on the way to work as I was going up an on-ramp (uphill) to get on the highway, the truck began to sputter and seemed like it was having a lack of power. Once on the highway there was a significant
change in the power and it began to sputter (especially in the first few
gears). While on the highway the engine light (which is always on probably
due to the fact that they put a different engine in the truck and it did not all
line up), started to flash. Then it went back solid again. Once I got off the
exit and was stopped at the red light, it began sputtering again and then
backfired slightly a few times. I made my way to my destination with
sputtering and a few small backfires (in the first few gears). Seems to have
the most trouble when stopped at light in drive idling and first few gears.
Then will drive fine but you can tell that it doesn’t have the same power.

I then took the truck to a gas station filled it up with premium (it was at
about ¼ of a tank before). Let it idle for ten to fifteen minutes and went to work.
Along the way same thing. Most of the sputtering and small backfire
sounds came mostly when stopped at light and going first few gears.

Note: there was some heavy rain yesterday and the truck is a bit low. I did
go through a few puddles yesterday on the way to work in the am. Never
noticed any changes after the puddles (about ten to fifteen minutes to my work). It
sat all day at work drove home just fine yesterday. No issues. Sat all night
then this morning drove it for two to five minutes before getting on the highway
and noticing the sputtering.

I checked the air filter and it is completely dry along with the inside of the
air filter container. My friend said it might be something to do with the wiring
and I might be able to see a spark if one of the wires is loose or not
connected properly. Not sure.

Any help would be greatly appreciated. Thank you!