You are mentioning fractions of pounds, most recipes in english units use pounds and ounces, if your fractional pounds were really ounces that would make a difference. E.g 3.4 pounds or 6-row or 3 lbs 4 oz?
I assumed 6.5 gal into kettle, 5.75 gal post boil, 5.5 gal transferred to fermenter, 75% mash efficiency. Beer Alchemy doesn't get into brewhouse vs mash efficiency, I believe this is brewhouse efficiency.
Given you got 5.5 gal of 1.042 wort it looks to me like your efficiency was 62%. If you really meant 3 lbs 4 oz then your efficiency was 66%.
So this is low but maybe not horrible. Probably some experience and a minor tweaks to your process will get you to a respectable efficiency. Here are some suggestions.
1. Work with a simple recipe while you figure out your issue...Something like a pale ale 10 lbs 2-row (US or British) and some C60 (8-16 oz depending on your preference). That should be a pretty reliable and repeatable mash, you can make a variety of beers by trying different yeasts and hops.
2. Look into your crush again. See if the supplier will double crush if you aren't crushing yourself.
3. Adjust your mash / sparge water so that you get equal amounts of run-off from first and second runnings. If you had added 3 quarts of hot water to the mash before running off first time you would have had 3.25 gallons of first runnings. Then you would have reduced your sparge water to 3.25 gallons to produce 3.25 gallons of second runnings for a total of 6.5 gallons into the kettle.
Good luck