Like a few others have pointed out...I'd bet that your grains (especially the chocolate malt) wasn't crushed. I had a friend do this exact thing a few years back to a Porter.
I'll tell ya whats not a bad brew day at all...doing an extract and all-grain batch in the same day. I have squeezed in an extract batch while waiting for my strike water to heat up and waiting for the 60 min mash on my all-grain batch. It doesn't add much time (if any) to your brew day.
I am with Yooper, just add the bulk (say 75%) of the extract after your 60 minute boil...at flameout. No reason to boil all that extract for 60 minutes.
Annapolis Homebrew is way overpriced...and they are using the same ingredients as everyone else.
My fav is Northern Brewer...I have also bought kits from Austin Homebrew...I prefer Northern's recipe's over AHS.
I have a 7 gallon round Rubbermaid Gatorade cooler that works perfectly. Brand new they can be expensive ($50-60), but I have seen used ones on ebay and craigslist for $20. I am surprised more people dont go this route instead of debating between 5 and 10 gallon coolers.
Nothing to do with your aluminum pot. I have stainless and aluminum pots...both are equally black on the bottom. The problem is that your (and mine) burner are very inefficient, resulting in a lot of soot on the bottom of our pots.
That's why the blow off tube is normally in place...to have a place for all that foam to go. I would have left it alone. Sounds like you are still okay.
Hefeweizens need to be at around 18 psi to carb well, I had the same exact problem a few weeks ago with my hefe. Cranked mine up to 18, and after a few days it was perfect.