I don't usually calculate it because I don't care but here is and example of how to figure brewhouse efficiency "let's say our expected gravity (at 100% efficiency) = 1.045, or 45 points. However we measured a gravity of 1.038 into the fermenter. Then our efficiency would be = 38/45 = roughly 84%." So as I figure it you are closer to 94% pretty respectable anyway.
Yes you will see a lot more gunk in the fermenter with AG, just the nature of the beast. It will settle down to the bottom so I do not filter it between the kettle and fermenter.
Try to get a reasonably clear sample in your hydrometer flask. Spin it to knock off any bubbles that might be hanging on and give it a minute. Most hydrometers need a 60°F sample but it should come with a conversion chart. Honestly I have take readings warmer then stuck the sample in the fridge to cool and did not find the difference listed. Then again if it's close to what I expected, I'm good with it. It will still come out beer, good beer.
Sounds like everything went extremely well. I wonder what the pH level of your spring water is.