1. Does anyone know if the Ford Performance Racing intake will be taller and thus reduce clearance and cause the throttle body to touch the underside of the hood?
No, the pi intake is the same height. Dorman is trash.
2. Will the PI upgrade require any reprogramming or other tweaking to the computer?
No, but it will work better.
3. Does this PI upgrade have any drawbacks beside the extra costs and heater hose extension?
Gas mileage will drop.
4. Any ideas about the minor power loss/ bogging down when I begin to accelerate from a dead stop? I have new injectors waiting be installed when I do the air intake manifold, but i didn't think it is fuel related from injector malfunction or blockage.
Any pending codes cause performance degradation, because it's having to make up for something not being right.
5. Has anyone had the fuel tank leakage issues after dropping the tank for replacement of the fuel pump?
The fuel pump hat is at an angle, and the gasket is bad. It will need to be replaced.
They reused the 20 year old one.
In your situation, I would:
Replace the front O2 sensors with OEM NTK sensors.
of the vacuum leaks. There are eight pieces of tubing in the evap line.
All are bad now.
When you do the intake, Carefully remove the EGR line from the TB, and Clean out all the egr passages in the TB.
Clean around the TB blade, including the back side. Gunk builds up there, and affects throttle response.
Buy a JY intake; as long as the mounting flange is still flat, it's all good.
While you're stealing the intake, steal the PI cams as well; those in NPI heads are a nice boost, degreed properly.
A Crown Vic or Gran Marquis intake is easiest to use, imho.
Do all the upgrades you want to do, Get Rid of all codes, and get it performing well before you Even think about a tune.
You can't fix engine problems with a tune; it will make it even more sensitive to Any problems that occur.
I accidentally tuned around a bad fuel pump, and was really rich on top end, lol.