Alright let me just start with I’m a mechanic for a living and this one has me stumped. 01 ranger 4.0 SOHC timing chain broke at 80 mph customer of my he wanted to just fix timing chain issue but found bent valves engine had 200k plus miles so we went ahead and just got a complete engine rebuild from the machine shop everything inside has been redone mains,rings,heads,everything. While engine was being built replaced fuel pump filter and flushed lines did everything right this isn’t my first time after everything that I did got everything back together have fuel have spark have compression have everything but engine will not start and run. Removed intake manifold to check injector spray and engine started up WITHOUT intake manifold yes WITHOUT intake manifold explain that to me put intake manifold back on and engine will not run just cracks and cranks no run have checked and tested everything here anybody else ever have this problem what am I missing here

 

 

Timing wouldn't be off, that's set by the crank shaft position sensor and cam shaft position sensor and they are not adjustable. Even if the CSP sensor was installed wrong it would still run.
To the OP:
If the truck runs with out the upper intake manifold, then you may have plugged the sensors in wrong.
Check your IAC valve and make sure it's opening when the key is on from cold.
Clean you MAF sensor.
Check your throttle position sensor.
Check for faulty wiring to the PCM.