22% Efficiency jump, 22% volume drop, feedback on this brewer growing up.

We have struggled with very poor efficiency thus far, getting around 60% and missing our gravities. FedEx brought the BarleyCrusher this week and we finally nailed our temps (153 after strike, lost about a degree during the entire hour). We got 82% efficiency doing a batch sparge! Awesome! We actually added water toward the end of the boil to bring the gravity down to 61 and to bring our volume up a bit.
We used two ounces of whole leaf hops in the boil and I think quite a bit of grist might have made it into the boil...there was a lot of gunk on the bottom of the kettle that we couldn't siphon into the carboy and we probably lost more than a gallon to it. We set the BC at .0035, and that may be too fine for the stainless steel false bottom we used, though it did appear to be running clear and we vorlaufed extensively. Since we've gone back to batch sparging I think I'll just put the bazooka tube back in the tun--I think it has a finer mesh.
Questions:
1. If that really was grist in the boil, does that cause off-flavors?
2. Is it better to use a hop bag for whole leaf hops during a boil to avoid all the gunk in the bottom?
3. Mash pH was 6.2. I wasn't prepared to lower it, but I did test it. Brewed the Haus Pale. What effect might that have?

1. Probably wasn't grain. Just out of curiosity, are you using a braid or manifold to filter in your lauter tun? When you boil, a lot of the proteins coagulate. The "hot break" falls out of solution and gunks up the bottom.

2. It does help with either whole or pellet. If you want to avoid the trub you should whirlpool. After you chill the wort use a long sanitized spoon to create a whirlpool in the kettle. Cover with sanitized foil and give it about 30 minutes to settle. If you do it right, the hot/cold break and hop mass should create a cone towards the center of the kettle. Its a little easier to siphon away from the concentrated trub mass this way.

3. Are you sure? Kaiser should be able to help you more here. I've never measured my mash pH, but I highly doubt it was 6.2. I was always under the impression that a normal grist would stabilize closer to the lower to mid 5 range unless your water is extremely jacked up.