Did I over torque the upper screws? The rail drops down a little from the receiver. Otherwise, everything else lines up great.
Not sure i follow on the over torquing part but do you have a carry handle? Using one really helps keep things aligned while tightening/torquing the screws. A larue or adm scope mount might work too.
ETA: Crap. Thanks for pointing that out. Lol!
Carry handle… 
It does help to use something to grip both the upper and the rail during installation.
Which upper receiver are you using?
MUR-1a. Its not off by much. It is just sitting a bit lower.
The bolt-up plate that sits behind the barrel nut on the RIS II should have enough vertical play while loose to attain proper alignment with the upper receiver’s rail. Just loosen all 6 screws and move it upward a touch before tightening them down again.
Alright. Ill try that. Thanks.
Yeah just loosen them enough to push the rail up some and torque them back down. You have to play a little with them to get them lined up perfectly.