Time to get back to square one. Been way too many mistakes so far ;)

Before any kind of accurate diagnosing can be done, the basics must be correct, which requires the correct parts, correctly installed.

AC Delco CR43TS spark plugs, with a gap of .045", torqued to 15 ft pounds.
AC Delco distributor cap & rotor. Put a dab of silicone dielectric grease on each terminal, inside and out, of the cap.
If the wires are over 5 years old, put new wires on it.

Double check the plug wire routing on the cap. Then triple check them. Pay close attention to wires for cylinders 1 & 3 on the cap, (post #13).

Aint that the truth lol

The wife drove it for 30Km with no water??
YOu might have a blown head gaskets....

that was what I originally thought to Bagherra but I think it blew out my water pump instead of the head gasket

Ok put in new spark plugs today it did not change the misfire condition

Are you certain that the cap is wired correctly?
What brand is the cap & rotor?

yes 100% wired correctly I can't remember the brand and my truck is like 30 klms from here so i will have to check next time im out there.

I'm thinking it could be the coil possibly or a sensor or a blown head gasket or something else that i just have no clue what it could be lol

All of the sensors, and the EGR valve, affect all cylinders equally. Both head gaskets would have to be blown to affect both cylinders 5 & 6, (they are on opposite banks). Not impossible, but not likely, especially without a coolant leak, or serious clouds of steam from the tail pipe when running. If 5 & 6 are dead, you're looking for something that is specific to those two cylinders. For example: Vacuum leak at the rear of the plenum, Spark plugs, plug wires, shorted out distributor cap, (not the rotor), fuel injector, valves, push rods, valve lifters, rocker arms. If the misfire on both cylinders happened simultaneously, the most likely cause would be the distributor cap is shorted. If you have a scan tool capable of viewing streaming data, posting the fuel trims, (long and short term) would be very helpful. Data at idle, and at 2000 rpm would be great.

I think we are getting beyond my scope I am in no way a mechanic. I just can't afford one so have no choice but to try it all on my own. But other then basic removal and installation of common parts I'm useless.The spider injector was a huge job for me. I might wait til I have a few extra bucks in a couple weeks and try to get it diagnosed again. I don't however think its just 5 and 6 now it's idling pretty low and rough but all the spark plugs I took out were black as hell not just 5 and 6 and they were only a couple weeks old tops it sounds really loud in my exhaust exhaust manifold gasket maybe would that make all my spark plugs black and cause it to run chitty i'm just grasping at straws here. also it does not backfire at all if that helps.

would me taking a video of it running tomorrow help at all?