Some thoughts on the OP:
-The sum of your mash and sparge volumes is 10G, and you say you got 6.5G into the kettle. If I have that right, it means your absorbtion/deadspace/leftover is 3.5G, which is a quite a lot even for the substantial amount of grain in your bill. That 3.5G sitting in your MLT has the same OG as your 2nd runnings, which in your case is probably pretty high because your sparge volume was quite low. That in itself is going to limit your efficiency substantially.
-Along those lines, you mentioned that you had 2qt remaining in the mash tun...I assume this is because you couldn't fit it all in the kettle? If I interpret what you're saying correctly, this is sugar you're throwing away and it directly affects your efficiency. You should certainly avoid doing that if you can.
-If you're not considering your water and mash pH, you probably should.
-You should be able to look at your crushed malt and conclude whether it's a possible issue. I bought my own mill, which I never thought I'd do, because even the LHBS that I love wasn't giving me consistently crushed grain. The grain looked "ok" for the most part after crushing at the shop, but now that I crush my own, the difference is painfully obvious. We can share photos here if you're not sure what it should/shouldn't look like.
I think you can definitely track down the source(s) of your problem if you want to, but it's going to require some work. Great beer does not depend on brewhouse efficiency, so as others have said it may not be that big a deal. With that said your numbers indicate that you're getting <60% brewhouse efficiency, and you really should be able to beat that if you'd like.
Hope this helps!