2013 F-150 XLT starts hard after sitting for a bit.

I'm trying to find somone who can help me.  I have
a 2013 F-150 5.0 Liter.  I recently installed K&N cold
air intake with DRY FILTER, a throttle body spaced
and Flowmaster Outlaw Exhaust.  After installing
cold air intake it just wouldn't start, just rolled and
rolled.  I took the truck back to stock with the
exception of exhaust, same issue.  I got it towed to
garage they replaced MAF Sensor and fuel pump.  
Got it back and started and ran great for a week.  
Now, it's starting again, I added all my mods back
on after it started acting up just being stock and got
a SCT X3 / 3015 to tune it thinking it was just
needing tuned.  Here's the thing...truck runs like a
rapped ape, I mean it's like a rocket...just doesn't
start easy.  It rolls and rolls and rolls then finally fires
up.  By that time everyone in the parking lot is
looking at me and if they weren't they are, the
exhaust is just nasty!  If I shut it off and turn it
immediately back on it starts right up, it's when it
sits for like 5 mins is when it has an issue starting.  
Anyone have any advice?