Found the problems
 

Well after much time on the phone with too many companies a conclusion has been found.

The quad box is fried and that is to get fixed. $25 if the resistor only $100 if the whole board. Not bad

The VP44 is the dragon flow and because the injector lines are not upgraded the fuel is not reaching the injectors at the correct time, duration and pressure. So those need to be upgraded.

For the time being the stock VP44 is going back on to get us going for the time being untill the lines are purchased. Not to mention is is winter here so no truck pulls for a few months.

I want to thank everyone for thier help and inform everyone of what the actual problem was

Did returning it to stock help then??

Returning it to stock helped slightly but still ran like junk. We will be taking it out here soon again with the stock pump reinstalled and going to see what happens.

Will keep you guys updated.

:tu:

Well initial conclution is that the stock pump is alrady running better...

Now just waiting for the roads to dry a little and will be taking it out to test.

It is better though already!!!

my 01 cracks like what you are talking about i am running 3000 tune but everything checks out nothing is wrong with mine infact in runs solid with the 3000 tune when i switched to this tune i started hearing the craking sound i can switch back and not hear it so i would think its normal for the pump stretch

Still running ok??

Yes it is running ok for now. This thread can be closed out I just wanted to finish filling it in with all the updates to cpmplete it....Hopefullly someone will search if they have a problem and this will help them.

Thanks Guys for alll the help.