As the problem was intermittent at first I kept clearing codes and driving, and now the intake gasket has shown itself as the culprit. Both banks lean, cyl 1,4,6 misfire, and it sounds like a blub blub in the exhaust so the cylinders are working but not great. With the repairs I've made it only leaves air to be the issue. It did start doing this right as it got cold so it's another victim of the annual Texas freeze like my slave cylinder was

 

I've popped a few hoods open before on a dark night and seen a spark show a few times. You could swap fuel injectors around and see if the code's move to another cylinder and check fuel rail pressure.

 

Funny enough i swapped the spark plug wires for 1 and 3 and the problem seems to be gone, not sure how my only guess is different length wires, however the speed at which electricity travels makes it make no sense.

 

Turns out it was all the start of a cylinder dying, it has approx. 45psi of compression, looks like I'm gonna have to run it till it quits then swap in a V8

 

You will also need to swap transmissions. The V6 transmission won't bolt up to a V8 unless you swap in an old 5.0 302. Electronics will be an issue.

 

Depending how deep the pockets are when it decides to go will dictate my options, like you said an old 302/351 would fit with minimal parts required(motor mounts and gauges), compared to a LS where there's everything different, since I do want to keep it manual I have the factory hole in the floor to line up with aswell.