I got it running again. I didnt do anything wrong originally. The problem was the plug to the coil on the new harness. It wasnt connecting correctly so i cut it off and spliced the old one on and it starts and runs everytime.

Thanks for all the help.

and for future reference, I did not swap the plug for the dist pickup and its working fine but if I have problems in the future i will look there first.
oh and this truck never had a clutch switch and I never had a problem with that

 

huh when I did my auto to manual swap I would not have messed with the crank sensor plug but past exp told me that the sensor is different for an A/T truck than a M/T truck I did not know what the difference was; and since doing the swap, I found out at least 1 difference (dont know if it is the only difference but I suspect not as it makes no sense to change the plug if the sensor is otherwise identical)

but the only reason I had to snip the plug on the engine harness side and splice one in from a M/T truck, is that the plug for an A/T is a mirror image of the M/T one they would not plug into the other tranny's sensor. Know how these "weather tite" plugs have locator tabs so that you can only plug them in one way?? It is "flipped over" as compared to the other one...if you understand what I mean.
I would not have screwed with it at all and just plugged it in as it was, if it were the same.... if yours is the same on the donor harness as the old one was then there is no need to mess with it.

 

I completely forgot about this until now. I actually cut the tab that was keeping it from plugging in off. since it was a mirror image i just sliced the new tab off so there is no tab at all and it fits great and it still seals.