I am assuming that this was occurring before you swapped boxes. A couple of things come to mind, and there are a couple of tests you can do to see which is the most likely culprit.
1) Failed Cascade (return) valve. This will cause the fuel in the lines to bleed back into the tank resulting in a hard start. The longer the truck sits, to a point, the harder it will be to start. The test is to park the truck facing down hill. This will keep the tank higher than the valve, keeping fuel from draining back as easily. Fix, new valve.
2) A fuel leak, similar symptoms to the top scenario, and just start by looking for wet spots.
3) Damaged fuel metering diaphragm inside the VP. When the vp is exposed to low pressure, the fuel metering diaphragm can travel up to 4x the designed distance that it is supposed to travel. This excess wear can cause the diaphragm to crack and become weak. Then when subjected to the higher pressure of a new stock, or performance lift pump, the metering diaphragm is overridden by the high pressure and it can't function as designed. When this occurs, the truck will have trouble starting when hot. The hotter the truck, and in my experience, the hotter the day, the harder it will be to start (I have no explaination for why ambient air temperature would have an effect on this). Cold starts will hardly be effected, and if shut down and immediately started again, there shouldn't be much issue either. The test for this. Sometime when the condition exists and the truck is having trouble starting, disconnect the lift pump circuit and try to start the truck again. If this is the problem, the truck will fire right up when the lift pump is not running. The truck should start like normal. If it does, immediately shut it down and plug the lift pump back in, so as not to damage the pump any further. Unfortunately, the metering diaphragm is not something that can be replaced without rebuilding the pump. If the metering diaphragm is the problem, there are a couple of fixes.
A) Wire in a switch to the lift pump. Wait until the truck is started, and then turn it on. This works but isn't my favorite solution. If for some reason someone else needs to drive your truck, it is a hassle explaining the switch that they have to remember to flip.
B) Wire in a N/O oil pressure switch that completes the circuit at 4-6psi oil pressure. This way the the truck has to be running in order for the lift pump to come on. But you have the added bonus that it comes on automatically.
Those are the places I would start looking. Hope this helps.
Sean
