I have my LL with a KNS protector.   The lower is milled for a LL or a sear (low shelf).  Without the upper on, when I put the LL with KNS protector in, I have plenty of room.  The LL isn't binding in the lower at all.  

I tried putting the upper on and it will not close.  I filed the rear lug down on the upper and it is more room.   What is holding me up is that the paddle is hitting the carrier and it will not close.  I can get a small Allen key in there and torque it so it works, but it's tight.   I did have the bolt milled (it's a 9mm) specifically for the LL.  

Without the KNS protector it is fine.   I'm not going to use it without it.    I've taken a bit off the rear lug.   I have room to file off more.  
What should be my plan of action?

W/O pics I am thinking the shelf may need a little tweaking ie; shaved (dremeled out.)

Having to shave the bottom of the lug for the re-enforcer is common. It is also common to have to fiddle with the carrier in order to tuck the paddle in between it and the back of the lug. I have one upper where I have to take the upper completely off, leave a little gap to tuck the paddle into, then push the upper on and back, inserting first the takedown pin, then the pivot pin up front.

LL is not as easy to take down or put back together as a factory sear or even a DIAS.

Many low shelf receivers require additional machining to the shelf, especially when a KNS protector is used.  The clearance issues are not just vertical,  but also toward the rear. Many receivers don't allow the RLL and KNS to move far enough to the rear to trip the disconnertor. M60Joe is one of the recommended ones to machine your lower for RLL/KNS clearance.

need photos please

I've LLs.
You need to grind off some metal from upper area where pin goes in.
Mine works like a Swiss watch.

Yea.  That's the issue.   Although the lower is a low shelf, it's not enough.  The LL fits without the KNS protector, so that settles it.  Now I need to get it milled out.

Pics would help a lot, but it is most likely that you just need to grind down the rear lug of your upper receiver more...especially since it works without the KNS protector installed.  I wouldn't mess with the lower for now.  In the meantime, take a depth measurement of your lower to see just how deep the shelf is cut.

Regarding the earlier post about clearancing the rear pocket of the lower, I have found that most receivers actually do not need it. It also prevents the use of the no-M16 parts select fire modification. It does help prevent the ears of the link from potentially banging against the receiver, which could possibly be either the main or contributing reason why links broke before the KNS protectors were used.  The KNS protector also prevents this type of damage.

Esox

RLL function check:

With the upper off, link installed and selector set to FIRE, or AUTO if using a modified FCG for select fire, press the trigger and cock the hammer back onto the disconnector.

If you can press back on the paddle area of the link with your other hand, and the link causes the disconnector to release the hammer, the lower is fine.