just brewed a guiness clone

I just brewed Guinness draught clone using the recipe in BYO 150 Classic Clones (extract w/grains). I took a sample to measure OG after I transferred it to the fermenter, topped it off, and stirred it. I got an OG of 1.028. My heart sank! I kept spinning the hydrometer to make sure it was correct. I even left it alone while I aerated the wort and pitched the yeast. I checked it again…Same. I decided that I would let it go overnight then check it again with a fresh sample. Then I decided to check now with a fresh sample. This time I got 1.039, witch is what beersmith said I should have. Is it better take OG after aerating and pitching yeast? I suspect that the addition stirring after pitching along with any additional mixing from the air pump and air stone helped with the mixing?

Also, The recipe called for light DME and light LME (late addition). I used all DME (adjusting amount for change), but my LHS only had extra light DME. I used it. The wort wasn’t as dark as I expected. Will the difference only be in color, or will it affect the taste?

Most likely the wort hadn't been completely mixed when you took your initial reading. I wouldn't worry!

I have the AG version of that recipe priming in bottles right now, it tastes spot on from what I remember Guinness USED to be.

The airlock was bubbling less than 2 hours after pitching the yeast. This morning I caught it as it was just starting to gusher, so I put together blow-off tube before left for work. I hope I get witin a few points fo the target gravity.