After I swap my engine in my Lincoln 2004 LS v8the

This problem will take some specific diagnosis that cannot be done online very well so you will need a repair shop with specialized equipment.

If it's blue smoke, your burning oil. Get the head gasket checked. If that's ok your looking at something more serious, (more expensive), inside the engine.

Could be the fuel filter located behind the left front wheel shield they tend to get blocked easy

Pull the MAF sensor and give it a cleaning the correct way.Sometimes something shorts those probes(tiny wires and delicate) and your engine will cut a shine on you.
Look up how to clean the MAF sensor if you don't know how. don-ohio

I have a 2004 LS V8

There all bad by now

Replace all the OEM Coils that are left

You have a Fuel Delivery Pump & a second Fuel Transfer Pump
in the fuel tank
The tank is large & under the car ,under the rear seat
Have to remove the exhaust system & drive shaft

The Fuel Pump Relay --is in the Battery Junction Box (BJB) as well
as the Fuel Pump Motor Diode

There also is a (REM) Rear Electronic Module
I recall that has a variable speed pump regulator
or whatever

There are even more players there as well

Very complicated system ,that you have no way to even
start on yourself
Doubtful even a repair shop could do much

I have a 2004 LS and all the Factory Manuals & Wiring
Diagrams. Without them your done

Check fuel pressure at rail on engine Should be about 42 lbs

remove dog house locate test port and install guage should be 45-60 psi

You have two pumps,I guess you know that ,if you already did one. Did you check fuel pressure at the rail and check out the electronic pressure regulator? What codes are coming up and do they stay set?

you need to check your fuel pressure

try 35psi in tires, max air pressure on goodyear tires is 44psi, chevrolet recomends 35psi